Download FUNCTIONAL CONSEQUENCES OF THE DIRECT PHYSICAL CBP/p300

FUNCTIONAL CONSEQUENCES OF THE DIRECT PHYSICAL
INTERACTION BETWEEN E2A TRANSCRIPTION FACTORS AND
CBP/p300
by
Brandy Dawn Hyndman
A thesis submitted to the Department of Pathology and Molecular Medicine
In conformity with the requirements for
the degree of Doctor of Philosophy
Queen’s University
Kingston, Ontario, Canada
September, 2007
Copyright © Brandy Dawn Hyndman, 2007
Abstract
The E2A locus is involved in chromosomal translocations associated with acute
lymphoblastic leukemia. The most common of these involves a translocation between
chromosomes 1 and 19 (t1;19), resulting in expression of the chimeric oncoprotein E2APBX1. A direct interaction between transcriptional activation domain 1 (AD1) of E2A
and KIX domain of the histone acetyltransferase (HAT) /co-activator CBP is required for
E2A-PBX1-mediated leukemia induction in mice. This thesis examines the functional
consequences of the direct, physical interaction between E2A and CBP, for both proteins.
We demonstrate that the interaction between E2A and CBP/p300, as well as another
HAT/co-activator, p/CAF, results in acetylation of E2A. Mutagenesis-based mapping
studies identify several lysine residues as substrates for acetylation. Of particular interest,
a conserved lysine (K34) located within AD1 is acetylated in vitro and in vivo.
Substitution of this residue to arginine impairs transcriptional activation of a luciferase
reporter while substitution to glutamine, mimicking the acetylation, restores E2Amediated transcriptional activation.
Recent studies have shown that several transcription factors can modulate the intrinsic
HAT activity of CBP/p300. We were surprised to find that E2A proteins enhance
acetylation of histones by CBP, in vitro and in vivo, in a KIX domain-independent
manner. Acetylation of E2A is also not required for stimulation of CBP/p300 histone
acetylation. It appears that E2A interacts with the other CBP domains to mediate this
effect, presumably through allosteric effects.
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In summary, we demonstrate that acetylation of E2A plays a role in mediating the
transcriptional activation activity of E2A. Furthermore, acetylation of E2A enhances its
interaction with CBP/p300, at least in the presence of additional nuclear factors. We
show evidence that p/CAF may mediate this effect. Enhancement of CBP/p300 HAT
activity by oncogenic E2A-PBX1 proteins in vivo, suggests that some of its leukemiapromoting effects may be due to E2A-induced gain of function effects on CBP/p300.
The enhanced interaction between acetylated E2A and CBP/p300, as well as the E2Amediated stimulation of histone acetyltransferase activity might play a role in the DNAbinding-independent induction of proliferation.
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Co-Authorship
Mr. Richard Bayly generated the results shown in Figure 12. Mr. Bayly was also
responsible for preparing some reagents. I performed all other experiments
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Acknowledgements
I have met many great people during my time a Queen’s University. First and foremost, I
would like to thank my thesis supervisor, Dr. David LeBrun, for allowing me to be a part
of his lab. He is very enthusiastic about research and I have learned a great deal from
him. David, I greatly appreciate your mentorship during the course of my PhD.
Since there is no ‘I’ in research, I would also like to acknowledge our excellent research
assistant, Mr. Richard Bayly. Dick always has a smile on his face and time to teach those
around him. I couldn’t have done it without your guidance. I’ll miss hearing about the
horses and the annual pond hockey games. Thanks also go out to all the past and present
members of the LeBrun lab, including Mr. Richard Casselman and Cheryl Foster.
I am also grateful to Ms. Barbara Saunders, the Graduate Secretary for the Department of
Pathology and Molecular Medicine, for letting me bend her ear over the years. (Yes Barb,
I checked the Graduate Handbook….)
Finally, and most importantly, I would like to thank my family for their unconditional
love and support. To Mom and Dad, I couldn’t have done it without your support and
encouragement. I love you both. Especially, thanks for the airmiles and plane tickets
home for the holidays over the past 8 years. Did it really take that long?! Kingston is
great city but Alberta will always be home. My brothers, Cody and Kyle, started their
PhD’s a year after me but gained the title of ‘Dr. Hyndman’ two years before me. I guess
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that’s the difference between Health Science research and Mathematics/Finance and
Economics! Thank you for your encouragement to get finished and for keeping life
interesting. Cody, maybe I’ll have time now to learn how to knit that sweater you’ve
been bugging me for over the past 10 years!
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Table of Contents
Abstract ............................................................................................................................... ii
Co-Authorship ................................................................................................................... iv
Acknowledgements ............................................................................................................. v
Table of Contents .............................................................................................................. vii
List of Figures ..................................................................................................................... x
Chapter 1 Introduction .................................................................................................... 1
Chapter 2 Literature Review ........................................................................................... 4
2.1 Structure and Function of the E2A Gene Products .................................................... 4
2.1.1 E2A Gene Products are Basic Helix-Loop-Helix Proteins ................................. 4
2.1.2 E2A Contains Two Transcriptional Activation Domains................................... 5
2.2 E2A Proteins Are Required For B-Cell Commitment And Differentiation ............ 10
2.2.1 E2A is Specifically Required for the Earliest Stages of B-Cell Differentiation
................................................................................................................................... 10
2.2.2 E2A is Involved in Later Stages of B-Cell Development ................................ 11
2.3 Regulation of E2A Activity..................................................................................... 11
2.3.1 Regulation of E2A by Dimerization with Other bHLH Proteins .................... 11
2.3.2 E2A Proteins are Substrates for Phosphorylation............................................. 12
2.3.3 E2A Stability is Regulated by Ubiquitination .................................................. 13
2.4 E2A Involvement In Translocations And Leukemia ............................................... 15
2.4.1 The E2A Gene is Located on Chromosome 19................................................. 15
2.4.2 PBX1 Structure and Function ........................................................................... 16
2.4.3 E2A-PBX1 Structure and Function .................................................................. 16
2.5 Chromatin and Transcriptional Regulation ............................................................. 18
2.5.1 Chromatin Structure ......................................................................................... 18
2.5.2 Enzymes That Covalently Modify Histones ..................................................... 19
2.5.3 Chromatin Remodeling Enzymes ..................................................................... 22
2.6 CBP and p300 are Transcriptional Co-Activator Proteins ...................................... 24
2.6.1 CBP and p300 Have Intrinsic Acetyltransferase Activity ................................ 27
2.7 Acetylation and Transcription Factor Regulation ................................................... 28
2.8 Recognition Motifs for Acetyltransferase Proteins ................................................. 29
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2.9 CBP Interacts Directly with E2A Proteins .............................................................. 30
2.9.1 Identification of E2A-CBP Interactive Domains.............................................. 30
2.9.2 Functional Significance of the E2A-CBP Interaction for E2A-PBX1-mediated
Leukemogenesis ............................................................................................... 32
Chapter 3 Hypothesis and Research Objectives .......................................................... 34
Chapter 4 Materials and Methods ................................................................................ 36
Chapter 5 Acetylation of Lysine 34 in E2A Proteins Contributes to Transcriptional
Activation ....................................................................................................... 47
5.1 Contributions ........................................................................................................... 47
5.2 Rationale.................................................................................................................. 47
5.3 Results ..................................................................................................................... 48
5.3.1 The Portion of E2A Included in E2A-PBX1 Interacts with Acetyl-Transferase
Proteins Capable of Acetylating Both Histones and E2A ................................ 48
5.3.2 Acetylation of E2A Correlates with Recruitment of CBP ................................ 52
5.3.3 In Vitro Acetylation of E2A ............................................................................. 57
5.3.4 Both p300 and p/CAF Interact Directly with E2A ........................................... 61
5.3.5 Acetylation of E2A Promotes its Interaction with CBP ................................... 64
5.3.6 Mapping of Acetylated Lysines ........................................................................ 67
5.3.7 Transcriptional activation by AD1 Involves Acetylation of K34..................... 78
5.3.8 A Role for Acetylation of Lyisne 34 in the Transcriptional Fynction of
Activation Domain ........................................................................................... 82
5.4 Discussion ............................................................................................................... 87
Chapter 6 E2A Enhances the Acetyl-transferase Activity of CBP ............................. 94
6.1 Contributions ........................................................................................................... 94
6.2 Rationale.................................................................................................................. 94
6.3 Results ..................................................................................................................... 95
6.3.1 E2A Proteins Enhance in vitro Acetylation of Histones by CBP/p300 ............ 95
6.3.2 Mapping of the E2A Domains Required to Increase HAT Activity of CBP . 103
6.3.3 The KIX and Bromo Domains are not Required for E2A-induced Increase of
CBP HAT Activity ......................................................................................... 107
6.3.4 E2A Does Not Enhance CBP Acetylation of Nucleosomes in vitro .............. 113
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6.3.5 E2A Enhances CBP Catalytic Activity in vivo............................................... 116
6.4 Discussion ............................................................................................................. 121
Chapter 7 General Discussion and Future Directions ............................................... 124
References ..................................................................................................................... 130
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List of Figures
Figure 1: Domain structures of E2A, PBX1 and E2A-PBX1 fusion proteins and location
of regulatory elements within E2A ..................................................................... 6
Figure 2: Histone modifications and Lysine acetylation ................................................ 20
Figure 3: Domain structure of the co-activator CREB-binding protein .......................... 25
Figure 4: E2A is acetylated by acetyltransferase activity recruitment from nuclear
extracts ............................................................................................................ 50
Figure 5: Acetylation of E2A correlates with recruitment of CBP.................................. 54
Figure 6: Acetylation of E2A by purified CBP/p300 or p/CAF ...................................... 58
Figure 7: p/CAF interacts directly with E2A. .................................................................. 62
Figure 8: Acetylation of E2A promotes its interaction with CBP/p300. ......................... 65
Figure 9: Schematic indicating the location and phylogenetic conservation of lysine
residues in the E2A-PBX1a oncogenic protein ............................................... 68
Figure 10: The catalytic domain of recombinant p/CAF acetylates lysines 34, 101 and
144 of E2A. .................................................................................................... 71
Figure 11: Recombinant p300 and the co-activator complex recruited from
nuclear extracts acetylate identical lysine residues within E2A amino acids
161-483. ........................................................................................................ 75
Figure 12: Post-translational modification of lysine 34 is involved in transcriptional
activation by E2A. ......................................................................................... 80
Figure 13: The oncogenic portion of E2A is not a substrate for ubiquitination or
sumoylation. ................................................................................................... 84
Figure 14: E2A enhances the histone acetyltransferase activity of p300. ....................... 98
Figure 15: Time course experiment showing that E2A enhances the catalytic activity of
CBP approximately two-fold ....................................................................... 101
Figure 16: The α-helical domain within AD1 and AD2 of E2A are dispensable for
enhancement of CBP histone acetylation. ................................................... 105
Figure 17: E2A interacts with the HAT domain of CBP to enhance intrinsic HAT
activity of CBP. The KIX and BROMO domains of CBP are dispensable for
enhancement of HAT activity by E2A......................................................... 110
x
Figure 18: E2A is unable to enhance CBP-mediated acetylation of nucleosomes in vitro
......................................................................................................................................... 114
Figure 19: The E2A portion of E2A-PBX1 mediates enhanced acetyltransferasedependent transcriptional activation by CBP in vivo. ................................... 118
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Chapter 1
Introduction
Leukemia remains the most common childhood cancer, accounting for approximately
twenty-five percent of all pediatric cancer cases in Canada (1). Acute lymphoblastic
leukemia (ALL), characterized by rapid accumulation of abnormal, often immature B- or
T-lineage cells in the bone marrow and blood, accounts for seventy-five percent of
childhood leukemias. While the current five year survival rate for pediatric ALL is
approximately eighty-percent, due to improved treatment protocols developed over the
last thirty years, ALL still represents the leading cause of cancer fatalities in persons
under the age of nineteen years (1).
Clues to the molecular mechanisms of leukemogenesis have been provided by the
discovery of non-random chromosomal abnormalities in the leukemic cells. More than
half of all leukemias have detectable chromosomal abnormalities by karyotypic analysis
(2). Some of these abnormalities are consistently associated with various sub-classes of
ALL; such non-random chromosomal translocations are seen in approximately forty-five
percent of ALL cases (2). Many of these translocations lead to juxtaposition of the coding
sequence of two genes, normally located on separate chromosomes, leading to expression
of chimeric oncoproteins. Translocations may also alter the regulation of a gene by
placing it under the control of new promoter elements.
One chromosomal translocation involving chromosomes 1 and 19, t(1:19), is found in the
leukemic cells of approximately five percent of ALL cases and is the second most
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common translocation in ALL. First reported in 1984, t(1;19) was determined to create a
fusion gene involving two genes, PBX1 on chromosome 1 (3,4) and E2A on
chromosome 19 (5). This translocation results in expression of a chimeric protein called
E2A-PBX1 and is found in approximately 30% of patients diagnosed with precursor Bcell ALL (pre-B ALL). This translocation was initially associated with a poorer
prognosis. However, more intensive treatment regimens have since erased this difference
(6). Interestingly, the E2A locus is also involved in at least two other leukemia-associated
translocations. A translocation between chromosomes 17 and 19 creates the fusion gene
E2A-HLF (7,8) while an internal rearrangement of chromosome 19 fuses the same region
of the E2A gene to the FB1 gene (9), resulting in expression of truncated forms of E2A.
E2A gene products normally function to regulate lymphocyte development by regulating
the transcription of B-lineage specific genes. In addition, E2A proteins can interact with
tissue specific factors to regulate tissue differentiation in other non-lymphoid cell types.
In recent years abundant evidence has suggested a functional interaction between E2A
and several transcriptional co-activator proteins in mediating E2A-target gene expression
(10-12). Work in Dr. LeBrun’s lab has uncovered a direct interaction between E2A and
the transcriptional co-activator CREB binding protein (CBP) (13). This interaction is
required for the induction of tumours in mice by E2A-PBX1 and the outgrowth of
immortal cells from primary bone marrow cultures (13,14).
Transcriptional co-activators, such as CBP and the highly homologous protein p300, are
involved in transcriptional regulation by two general mechanisms. First, by affecting
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chromatin conformation by acetylation of lysine residues within nucleosomal histone tails
and, second, by mediating recruitment of the initiation complex to promoters through
interaction with DNA binding transcription factors. Over the past decade several
investigators have determined that CBP/p300 can also mediate acetylation of non-histone
proteins such as transcription factors (15). This acetylation has been shown to affect
several aspects of transcription factor function, including DNA binding affinity, proteinprotein interactions, sub-cellular localization and protein stability. Reciprocally,
interaction of several viral and cellular proteins with histone acetyltransferase (HAT) coactivators, including CBP/p300, alters the ability of the co-activator to acetylate histone
proteins.
The work described in this thesis investigates the functional consequences of the direct
physical interaction between E2A and CBP/p300. The overall, longer-term objective is
the elucidation of potential novel mechanisms of leukemia induction by E2A-proteins
and, consequently, the identification of new targets for therapeutic intervention.
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Chapter 2
Literature Review
2.1 Structure and Function of the E2A Gene Products
2.1.1 E2A Gene Products are Basic Helix-Loop-Helix Proteins
The E2A gene products, E12 and E47, referred to herein as E2A proteins, represent the
founding members of the basic helix-loop-helix (bHLH) family of transcription factors.
The carboxy-terminus of E2A proteins contains two regions of conserved hydrophobic
residues separated by a linker sequence (16). Examination of these residues using a
helical representation revealed two amphipathic helices separated by the linker sequence
containing amino acids characteristic of a loop structure. This motif was subsequently
designated as helix-loop-helix (HLH) (16). Additional structural analysis revealed a
region of basic amino acids immediately amino-terminal to the HLH motif (17)
responsible for mediating interaction with the major groove of DNA, while the HLH
structure mediates homo- or hetero- dimerization of two HLH containing proteins.
Dimerization of bHLH proteins is independent of DNA binding, however dimerization is
essential for DNA binding at the consensus DNA sequence CANNTG. This sequence,
named the E-Box, was originally identified in the enhancers of the immunoglobulin
heavy chain (IgH) and kappa light chain genes (18-20) but has since been found in a
variety of other cell-type specific gene promoters and enhancers.
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Several other bHLH containing proteins have been identified since the identification of
the bHLH domain in E2A proteins. These have been characterized based on structural
similarities, tissue distribution and interaction with other HLH containing proteins. E12
and E47 belong to Class I bHLH proteins. This class of proteins is widely expressed in
many tissues and includes the related proteins HEB, E2-2 and Drosophilia protein
daughterless (da) (16). Class I proteins heterodimerize with Class II bHLH proteins. The
latter show restricted expression in specific tissues or developmental stages. MyoD
(21,22), MRF4 , Myf5 and myogenin (23), for example, are muscle specific bHLH
proteins involved in regulating myogenic differentiation in combination with E2A
proteins; specifically, MyoD forms heterodimers with E2A proteins (24).
2.1.2 E2A Contains Two Transcriptional Activation Domains
E2A proteins are proposed to function as transcriptional activators mediating expression
of target genes containing E-Box elements. Henthorn et al (25) noted in yeast and
mammalian cells that the amino terminal two-thirds, i.e. the portion not encoding the
bHLH domain, of the E2A splice variant E2-5 and a related bHLH protein E2-2 were
required for transactivation of reporter genes, suggesting the presence of transcriptional
activation domain(s) in this region (25). Mapping studies using transient co-transfection
of portions of E2A protein fused to the DNA binding domain of the yeast transcription
factor GAL4 identified two independent transcriptional activation domains, AD1 and
AD2, capable of inducing expression of a reporter gene. AD1 is located at the extreme
amino terminus (amino acids 1-99) (10,26) while AD2 is centrally located (amino acids
394-406) (26,27) (Figure 1a). Originally considered to function independently, more
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Figure 1: a) Domain structures of E2A, PBX1 and E2A-PBX1 fusion proteins. The
numbers indicate the first and last amino acid positions in a domain or protein. The
vertical line represents the fusion point between E2A and PBX1 proteins. AD, activation
domain; bHLH, basic helix-loop-helix domain; HD, homeodomain; vertical red lines
indicate amino acid differences in E47 compared to E12. b) The genomic E2A locus and
location of protein domains or amino acids involved in the regulation of E2A
function. Black lines represent exons. Exon 1 contains sequence for a 5’ untranslated
region (UTR) as well as the translation start site. Exons 2-16 are coding exons. The blue
and red boxes represent the alternatively spliced E12 and E47 exons (17a and 17b)
encoding the helix-loop-helix domain of the proteins. A small part of exon 18 is also
encodes the C-terminus of the protein as well as a large 3’UTR. * indicates a nuclear
localization signal (NLS); # indicates a inhibitory domain involved in inhibition of DNA
binding by E12 homodimers; S, serine residues known to be phosphorylated.
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recent evidence from the LeBrun Lab suggests AD1 and AD2 act co-operatively to
promote maximal E2A transcriptional activation (13).
Activation domain 1 contains a stretch of highly conserved amino acids that form a
potential α–helical domain located from residues 11-28 of E2A proteins. Mutagenesis of
residues within the region that disrupt the α–helical conformation dramatically reduces
the transcriptional activation capability of AD1 in both yeast and mammalian cells,
indicating that the helix located within AD1 is required for transcriptional activation and
interactions mediated by this domain are conserved between mammals and yeast (10,13).
Located within the α–helical region of AD1 is Leucine-Aspartic Acid-PhenyalanineSerine (LDFS) motif that is highly conserved in class I HLH proteins, including E2A
(10). Mutation of the LDFS motif (amino acids 20-23) significantly impairs
transcriptional activation of reporter genes in yeast and mammalian cells (10). In
addition, AD1 interacts with the SAGA co-activator complex in yeast in a manner that
requires an intact LDFS motif (12). This interaction is required for transcriptional
activation by AD1 in yeast, suggesting a role for co-activator complexes in E2Amediated stimulation of transcription. A highly conserved LXXLL (where X represents
any amino acid, amino acids 16-20) is also present in this region of AD1. The LXXLL
motif was first identified in nuclear hormone receptors as a binding site for co-activator
proteins (28,29) further supporting a role for transcriptional co-activator complexes in
E2A function.
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2.2 E2A Proteins Are Required For B-Cell Commitment And Differentiation
2.2.1 E2A is Specifically Required for the Earliest Stages of B-Cell Differentiation
A role in lymphocyte development was suggested by the original identification of the
E2A proteins as immunoglobulin enhancer-binding proteins (16). Furthermore, ectopic
expression of E2A in a macrophage cell line induces a more B-cell like phenotype (30)
and over expression of E2A in a pre-T-cell line stimulates low but detectable levels of
transcription and rearrangement of the immunoglobulin heavy chain gene (31).
E2A knockout mice show severe reduction of B-lineage cells. Rearrangement of the
immunoglobulin heavy chain segments is also absent, indicating that B-cell
differentiation is blocked before the pre-B-cell stage (32,33). Expression of several genes
that are regulated by E2A, and required for B-cell differentiation, is also significantly
decreased in the knockout mice (34). In addition, mutant E2A protein lacking
transcriptional activation domains but containing the bHLH domain is unable to induce
expression of immunoglobulin genes or of several genes normally regulated by E2A,
supporting the notion that the biological function of E2A requires the activation domains
(30). Together, these results demonstrate a crucial role for the E2A proteins in promoting
early stages of B-lymphoid development through regulating genetic recombination at the
immunoglobulin loci and transcription of key target genes (34).
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2.2.2 E2A is Involved in Later Stages of B-Cell Development
In addition to being highly expressed (35) and active in early B-cell lineage commitment
and differentiation (36), E2A shows increase mRNA levels in germinal centers (37) and is
detectable in all secondary lymphoid tissues (38,39). Naïve mature B-cell express low
levels of E2A proteins while activation of these cells results in induction of E2A protein
expression and DNA binding (40). In addition, active B cells lacking E2A activity (i.e.
DNA binding) fail to undergo immunoglobulin class switching (40). Together, these
results indicate that E2A is also required at later stages of B-cell development.
2.3 Regulation of E2A Activity
E2A proteins are expressed broadly in tissues and play a role in mediating differentiation
of B-lymphocytes as well as muscle and other cells types (37,41). In addition, E2A plays
a role in growth control, as over expression inhibits cellular proliferation and mediates
cell cycle arrest (42). E2A levels are elevated in G0 arrested cells and decline with cell
cycle progression, suggesting that E2A protein levels and/or activity must be downregulated for cell cycle progression (43).
2.3.1 Regulation of E2A by Dimerization with Other HLH Proteins
E12 and E47 are generated by differential splicing of a single exon encoding the bHLH
domain (Figure 1b). The bHLH domains of E12 and E47 show 80% amino acid identity
(16), and the exons encoding the more amino-terminal polypeptide elements are invariant
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in the isoforms E12 and E47.The differences in the basic DNA binding and HLH
dimerization domains raise the possibility that these differences affect DNA binding and
oligomerization with other proteins. In B-lymphocytes, E47 homodimers are stabilized by
an inter-molecular disulfide bond and bind to DNA (44,45) while E12 proteins are less
able to homodimerize and bind E-Box elements (16,24). Consistent with these
observations, an inhibitory domain was identified in E12 that prevents it from forming
homodimers but has no affect on heterodimerization with other class I and class II HLH
proteins (46).
A class of HLH proteins that lack a basic region has been identified and named Id, for
Inhibitor of DNA binding (47). These proteins dimerize with E12, E47 and other bHLH
proteins through a HLH domain, resulting in dramatically decreased DNA binding and
transcriptional activation by heterodimers. Id expression is highest in immature
progenitor-B (pro-B) cells and decreases as the cells differentiate to pre-B and mature Bcells (48,49). This pattern of expression correlates with up-regulation of E2A levels and
function. In addition, over expression of Id1 in B-lineage cells impairs B-cell
development in a mouse model (47,48) reminiscent of the phenotype seen in E2A
knockout mice (32,33). Therefore, Id proteins appear to function physiologically as
dominant-inhibitory regulators of E12/E47 function (47).
2.3.2 E2A Proteins are Substrates for Phosphorylation
Protein phosphorylation regulates transcription factor function in a variety of ways,
including by modulating DNA binding, protein-protein interactions and by targeting
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transcription factors for proteolytic degradation (50). E2A proteins are phosphorylated in
B-lymphoid and non-lymphoid cell lines (51). Further investigation revealed that
phosphorylation at two serine residues (serine 514 and 529) of E47, adjacent to the bHLH
domain, inhibits DNA binding by E47 homodimers but not E47/MyoD heterodimers
(52). In addition, these two serine residues are hypo-phosphorylated in B-lineage cells
compared to non-B-cells thus allowing DNA binding by E47 homodimers (53).
In muscle progenitors, phosphorylation of E2A by the p38 kinase results in inhibition of
E2A/MyoD transcriptional activation and myogenesis without effecting DNA binding,
heterodimerization or protein levels (54). E2A proteins are also phosphorylated by
several G1 cyclin-dependent kinases at amino-terminal serine residues (serine 48 and
serine 154) to relieve E2A mediated growth suppression and allow entry into the cell
cycle through a mechanism that does not affect E2A transcriptional activity or DNA
binding (55). These results suggest that E2A proteins are regulated by phosphorylation
downstream of signaling pathways that respond to extracellular signals or to cell cyclerelated cues.
2.3.3 E2A Stability is Regulated by Ubiquitination
Regulated protein degradation is accomplished in cells through the ubiquitin-proteasome
system (56). Ubiquitination of proteins involves a three step process culminating in
covalent conjugation of the conserved 76 residue polypeptide ubiquitin to the ε-NH3+
group of lysine residues. Ubiquitin activating (E1) enzymes activate ubiquitin to generate
13
an E1-ubiquitin intermediate. Ubiquitin conjugating (E2) enzymes then transfer the
ubiquitin from E1 to generate an E2-ubiquitin substrate that is specifically bound by an
ubiquitin ligase (E3) enzyme complexed with the final substrate protein. The E3 enzyme
transfers the ubiquitin to the ε-NH3+ group of a target lysine. Poly-ubiquitinated chains on
lysine residues target proteins to the 26S proteasome where they are proteolytically
degraded (56).
E2A proteins contain three proline glutamine/aspartate, serine, threonine (PEST) rich
regions, located within the bHLH region, within AD1 (amino acids 47-67) and at amino
acids 169-189 (Figure 1b). PEST regions are commonly found within rapidly degraded
proteins (57). E2A proteins interact with UBC9, a SUMO conjugating enzyme (58-62), in
a manner that requires a bipartite binding site located at amino acids 476-494 and 505513, amino-terminal to the bHLH domain (Figure 1b) (63,64). Treatment of cells
expressing E2A with proteasome inhibitors stabilizes E2A, as does anti-sense RNA to
UBC9, suggesting that E2A is degraded through the proteasome (64,65). SUMOconjugation is not normally associated with degradation and E2A-SUMO conjugates
have not been described suggesting that the E2A degradation domain (i.e. the UBC9
interactive region) may also be a recognition site for conventional ubiquitin conjugating
enzymes or the E2A-UBC9 interaction may be a necessary intermediate step in the
degradation pathway (65).
Deletion of the UBC9 interacting region stabilizes E2A proteins and results in
accumulation of hyper-phosphorylated E2A, suggesting that phosphorylation may be a
14
prerequisite for degradation of E2A through the proteasome (65). In fact, Notch-1induced inhibition of E2A transcriptional activity is a result of the induction of E2A
ubiquitination and proteosomal degradation in a manner that requires the activity of MAP
kinases (66-68). In addition, E2A phosphorylation promotes an interaction with Skp2 and
the SCFSkp2 E3 ubiquitin ligase complex (66,69).
2.4 E2A Involvement in Translocations and Leukemia
2.4.1 The E2A Gene is Located on Chromosome 19
Using in situ DNA hybridization of a radio-labeled E47 probe to human metaphase
chromosomes, Mellentin et al localized the E2A gene to the short (p) arm of chromosome
19 at band 13.2-13.3 (5). This region of chromosome 19 had previously been implicated
in one of the most frequently reported chromosomal translocations associated with ALL,
t(1;19)(q23,p13.3), described by several groups in 1984 (70-72). The E2A gene was
further mapped to the breakpoint on chromosome 19 in eight leukemia specimens and
two cell lines positive for the 1;19 translocation (5). Analysis of the RNA from one cell
line indicated a larger than expected E2A mRNA, suggesting the existence of an E2Afusion gene in t(1:19)-positive leukemia cells and a pathological role in leukemogenesis
(5). Sequencing of cDNAs representing fusion transcripts identified the translocation
partner as PBX1 (3,5).
15
2.4.2 PBX1 Structure and Function
The PBX1 gene was discovered and cloned as a result of its involvement in the 1;19
translocation (3,4). The gene product, PBX1, is a member of the three amino acid loop
extension (TALE) class of homeodomain (HD) proteins (73). Differential splicing at the
extreme 3’ end of the PBX1 pre-mRNA results in expression of two protein products,
PBX1a and the shorter PBX1b (Figure 1a) (3,4). PBX1 interacts with a conserved
hexapeptide sequence of HOX proteins located adjacent to the HOX HD (74-76).
Reciprocally, HOX proteins interact with the three amino acid insert located within the
PBX1 HD. HOX-PBX1 heterodimers co-operatively bind to overlapping DNA binding
sites on opposite faces of the DNA (77) to regulate expression of genes involved in
determination of cell fate and embryonic development (78). Importantly, PBX1 is not
normally expressed in B-cells (79).
2.4.3 E2A-PBX1 Structure and Function
The chimeric oncoprotein E2A-PBX1 consists of the N-terminal two-thirds of E2A,
including its two transcriptional activation domains, fused in frame to most of the PBX1
protein, including its DNA binding homeodomain (Figure 1a) (3). The E2A-PBX1
oncoprotein is a potent transactivator in several studies (80,81). In the most intuitive
model of E2A-PBX1 mediated leukemogenesis, DNA binding of E2A-PBX1 occurs at
PBX1-defined target sites and is mediated by the PBX1-derived homeodomain. The
activation domains of E2A recruit co-activators and the general transcription machinery,
16
thereby activating expression of genes not normally expressed in B-lymphocyte
progenitors. This abnormal gene expression pattern is thought to disrupt B-cell
development, causing leukemia (80-82). However, it has been demonstrated that deletion
of the DNA binding domain HD from E2A-PBX1 does not abrogate growth deregulation
in fibroblast or induction of malignant lymphomas in transgenic mice (79,83). In fact,
replacement of the entire PBX1 portion of E2A-PBX1 with DNA-binding and
dimerization domains from the yeast transcription factors GAL4 or GCN4 also does not
abrogate transformation of cultured fibroblasts. Forced homodimerization of E2A 1-483
in fibroblasts is capable of causing growth deregulation, suggesting that PBX may, at
least in part, contribute to oncogenesis by mediating oligomerization of E2A domains
(84). In contrast, deletion of the E2A-derived transcriptional activation domains from the
chimeric protein abrogates the oncogenicity of the protein (13,79,84). These results
suggest that interactions mediated by the E2A portion of E2A-PBX1 may be more
important than DNA binding mediated by PBX1 at least for growth deregulation by the
protein. In an alternative model proposed for E2A-PBX1 induced leukemogenesis, the
E2A portion interacts with transcriptional co-activators and, perhaps in a dominantinhibitory manner, sequesters these key co-activators from wild-type E2A or other
transcription factors with tumour suppressive functions (85). Disruption of transcription
factor/co-activator interactions could result in altered gene expression at many loci and
contribute to development of leukemia (12,25,84). These two proposed oncogenic
mechanisms are not mutually exclusive and leukemogenesis by E2A-PBX1 likely
involves aspects of both models.
17
2.5 Chromatin and Transcriptional Regulation
2.5.1 Chromatin Structure
Nucleosomes represent the smallest unit of DNA compaction. They consist of 147 base
pairs of DNA wrapped 1.65 turns around an octamer of core histones. Each nucleosome
contains two units of each of the core histones, H2A, H2B, H3 and H4 (86). Individual
nucleosomes are joined by a short segment of linker DNA of approximately 10 to 80 base
pairs in length. This linker DNA is bound and stabilized by histone H1 proteins and the
nucleosomes are then further compacted into higher order chromatin structures. These
exclude other proteins from interacting with DNA and must be modified in order for the
DNA to become more accessible to transcription factors, the RNA polymerase II
initiation complex and the DNA replication machinery (87,88).
In eukaryotic organisms, gene transcription must be highly regulated so as to ensure that
genes are expressed at the proper time and in the correct cell-types. Gene transcription is
regulated by sequence specific DNA binding of transcription factors to promoter sites
followed by recruitment of co-regulatory complexes and consequent repression or
enhancement of gene transcription (89). Transcriptional initiation requires alteration of
the chromatin structure and recruitment of the basal transcription machinery. Two general
classes of co-regulators have been described: a) those that covalently modify histones;
and, b) ATP-dependent chromatin remodelers (90).
18
2.5.2 Enzymes That Covalently Modify Histones
While the structured globular domains of the histone octamer are located within the
nucleosome particle, flexible amino-terminal histone tails extend freely from the core.
These histone tails are positively charged, lysine rich and contain sites amenable to posttranslational modifications important for chromatin function. Several different
modifications have been identified on histones, including: acetylation, methylation,
sumoylation, ubiquitination and phosphorylation (Figure 2a). Perhaps the two best
characterized histone modifications are acetylation and methylation (91).
Actively transcribed genes are associated with increased histone acetylation while
heterochromatic, untranscribed regions of the genome are typically associated with hypoacetylated histones (92,93). Several enzymes have been identified that are able to transfer
an acetyl group from acetyl-co-enzyme A to the ε-NH3+ group of lysine residues, mainly
in the histone tails (Figure 2b). These enzymes, called histone acetyltransferases or HAT
proteins (94), can be recruited to promoters by interaction with sequence-specific DNA
binding transcriptional activators (87,88). Subsequent acetylation of the surrounding
nucleosomal histones and the non-histone, chromatin-associated high mobility group
(HMG) proteins (95,96) neutralizes the positive charge of the lysine residues, affecting
the contacts between histones, histone and DNA as well as binding of regulatory proteins
to acetylated chromatin (94). Acetylation of lysine residues is a reversible process and
another group of histone modifying enzymes, the histone deacetylases (HDACs) are able
to remove the acetyl group allowing the DNA to return to the repressive state (97).
19
Figure 2: Histone Modifications and Lysine Acetylation. a) Nucelosome core particles
showing 8 N-terminal tail domains. Post-translational modifications known to occur on
each tail are indicated by coloured symbols. Modified from (98) b) Histone
acetyltransferase (HAT) enzymes are able to catalyze the transfer an acetyl group from
acetyl-co-enzyme A to the ε-NH3+ group of lysine residues resulting in the neutralization
of the positive charge of the lysine residues.
20
21
Histone methylation is also implicated in transcriptional control. Methylation occurs at
lysine and arginine residues by a class of enzymes called histone methytransferases
(HMTs) and can be either repressive or activating, depending on the specific lysine or
arginine modified in each histone. To make matters more complex, HMT enzymes can
add one, two or three methyl groups to each substrate amino acid. As with acetylation,
methylation of lysines and arginines is reversible by several demethylating enzymes (99).
Both acetylation and methylation create binding sites for protein-protein interactions,
resulting in recruitment of additional factors involved in transcription. Acetylated lysines,
for example, are recognized by bromodomains of chromatin-interactive proteins while
methylated residues are recognized by chromodomains. Both bromo- and chromodomains are found in many histone modifying enzymes as well as in components of the
ATP-dependent remodeling complexes and the basal transcription machinery (99).
2.5.3 Chromatin Remodeling Enzymes
Chromatin remodeling enzymes are found within large multi-subunit complexes and
function to reposition DNA on nucleosomes. All chromatin remodeling complexes
contain an ATPase subunit belonging to the SNF2 superfamily of DNA helicase/ATPases
and use the energy from ATP-hydrolysis to alter protein-DNA interaction. The two best
characterized sub-families of ATP-dependent remodeling complexes are: 1) SWI/SNF;
and, 2) ISWI (100).
22
The SWI/SNF complex was first described in yeast as a regulator of mating type
switching (101). Human homologues have subsequently been described and are involved
in regulating gene expression. SWI/SNF-type complexes contain subunits capable of
interacting with DNA and histones. The histone binding activity is mediated by a
bromodomain found within the catalytic subunit, that recognizes acetylated lysines in
histone tails. In addition to interacting with acetylated histones, SWI/SNF complexes
interact with components of the basal transcription machinery and RNA pol II and are
generally localized to actively expressed genes (102). SWI/SNF complexes are also
known to interact with sequence-specific DNA-binding transcriptional activators (102).
For example, acetylation of erythroid Kruppel like-factor (EKLF) by CBP enhances its
interaction with the SWI/SNF complexes resulting in enhanced transcriptional activation
(103).
Unlike the SWI/SNF complexes, ISWI complexes have not been found to associate with
RNA pol II and have been suggested to reposition nucleosomes to establish a repressive
chromatin environment. ISWI complexes are primarily associated with non-transcribed
regions of the chromatin (104) and contain an activity not present in SWI/SNF type
complexes, the ability to generate regularly spaced nucleosomes. This suggests that ISWI
type complexes play a role in maintaining chromatin structure (100). However, recently
ISWI components containing plant homeodomain (PHD) motifs were shown to be able to
recognize histone 3 (H3) tri-methylated at lysine 4 (H3K4me3) (105,106), a histone
modification associated with transcription start sites of active genes (107). These results
23
suggest that activation or repression of gene transcription by ISWI complexes is promoter
dependent (100).
2.6 CBP and p300 are Transcriptional Co-Activators
Two of the most widely studied transcriptional co-activators are CREB binding protein
(CBP) and p300 (Figure 3). CBP is a large (265 kDa) protein that was originally
identified in a screen for proteins that interact with the phosphorylated form of the
transcription factor CREB (108). The phospho-CREB-CBP interaction stimulates CREBmediated expression of a target gene over that induced by unphosphorylated CREB
(109,110). p300 was identified as an adenoviral E1A interacting protein (111,112).
Analysis of the p300 and CBP amino acid sequences reveals that the two proteins are
highly similar, especially over a centrally located 800 amino acid span (85% identical,
95% homologous) (113). This region includes a bromodomain as well as the C/H3 region
identified by Eckner et al as responsible for p300 binding to E1A (114). Since CBP and
p300 are highly identical and can substitute for one another in many, although not all,
functional assays, they are often referred to collectively as CBP/p300 (115,116).
Several studies have also determined that CBP and p300 are capable of interacting with
the basal transcription factors TFIIB (109,117) and TATA binding protein (117,118) and
form a complex with RNA polymerase II (119-122). Along with the evidence that CBP
and p300 stimulate transcriptional activation by CREB (109,110), these results support
the idea that CBP/p300 are transcriptional co-activator molecules.
24
Figure 3: CREB-binding protein (CBP) organization and interactions. C/H,
cysteine/histidine rich regions 1-3; The KIX domain mediates interactions with a large
number of transcription factors including CREB, c-Myb and E2A. The bromodomain
(BROMO) mediates protein-protein interactions by association with acetylated lysines.
HAT, the region of CBP containing histone acetyltransferase catalytic activity. TAZ, a
zinc-finger domain involved in interactions with multiple proteins. Some known CBPinteracting proteins, discussed in this thesis, are indicated below the functional domains.
The numbers represent the first and last amino acids of domains or the human CBP
protein.
25
26
2.6.1 CBP and p300 Have Intrinsic Acetyltransferase Activity
One mechanism of CBP/p300 mediated stimulation of transcription was postulated to be
through recruitment of the p300/CBP Associated Factor (p/CAF) to promoters. p/CAF
was cloned based on homology to the yeast GCN5, a transcriptional co-activator with
intrinsic AT activity (123,124). Like GCN5, p/CAF also efficiently acetylates the free
core histones H3 and H4 as well as nucleosome particles (123). p/CAF was subsequently
shown to interact with p300 and CBP at a region adjacent to the E1A binding site (123).
In fact, binding of p/CAF to CBP/p300 inhibits binding by E1A in a competition assay
and E1A is able to disrupt the p300-p/CAF interaction in vivo (123).
Based on this discovery, E1A was used as a ligand to recruit interactive proteins from
nuclear extracts. E1A recruits significant amounts of HAT activity while an E1A mutant
unable to interact with CBP/p300 cannot recruit HAT activity (125). Recombinant p300
and CBP were subsequently tested for their ability to acetylate histones. A region located
between the bromodomain and the E1A binding site that is 91% similar between CBP
and p300 was identified as the HAT catalytic domain (126). Unlike p/CAF, p300
preferentially acetylates H4, suggesting that the two HAT proteins may co-operate to
acetylate histones at promoters. The HAT domain of CBP/p300 does not show any
sequence similarity to the HAT domains of GCN5 and p/CAF, consistent with CBP/p300
and GCN5/p/CAF belonging to separate families of HAT proteins (125).
27
2.7 Acetylation and Transcription Factor Regulation
Acetylation of histones has been convincingly identified as a key modulator of
transcriptional activity. Hyper-acetylated histones are consistently associated with
actively transcribed genes while hypo-acetylation and recruitment of HDAC enzymes is
associated with a repressive chromatin state (99). Beyond histones, a growing list of nonhistone proteins have been identified as substrates for acetylation by co-activators,
including CBP/p300 and p/CAF (15,127).
Acetylation of transcription factors has been demonstrated to have a variety of functional
effects and has been postulated to be as important a regulator of protein function as
phosphorylation (128). Acetylation of lysines can have positive or negative effects on
protein interactions with DNA. For example, acetylation of lysines adjacent to the DNA
binding domain of p53 results in enhanced DNA binding (129) while acetylation within
the DNA binding domain of High Mobility Group 1 protein (HMG1) antagonizes DNA
binding, likely by neutralizing a positive charge that contributes to interaction with
negatively charged DNA (130).
Acetylation also plays a role in regulating protein-protein interactions by transcription
factors. Acetylation of MyoD, for example, results in a higher affinity interaction with the
bromodomain of CBP/p300 (131). Acetylation is also able to destabilize protein-protein
interactions. The interaction between the nuclear hormone receptor co-activator ACTR
28
and promoter-bound estrogen receptor is disrupted by acetylation by CBP, resulting in
down regulation of transactivation (132).
Poly-ubiquitination of lysines targets proteins for degradation by the proteasome. Since a
particular lysine residue cannot have two post-translational lysine modifications
simultaneously, prior acetylation can antagonize ubiquitination, thereby affecting protein
stability. For example, several lysine residues in p53 are substrates for both ubiquitination
and acetylation. Acetylation of p53 prevents ubiquitination and stabilizes p53 (133,134).
In conclusion, transcription factors are direct substrates for acetylation by transcriptional
co-activator/acetyltransferases and this modification is capable of altering transcription
factors function through multiple mechanisms, including effects on DNA binding,
proteins stability, sub-cellular localization and protein-protein interactions (15).
2.8 Recognition Motifs for Acetyltransferase Proteins
Examination of a large number of polypeptide sequences that are acetylated by various
HATs has failed to uncover a strictly conserved consensus recognition motif. Therefore,
it is not possible to identify potential acetylation sites by sequences analysis alone (94).
Some evidence exists to suggest that lysine (K) preceded by glycine (G), alone (135) or
as part of a larger GKXXP motif (where X equal any amino acid and P represents
proline), represents a weak consensus for lysine acetylation for CBP/p300 and p/CAF
(94).
29
Another potential consensus, KX1-2XKK, is apparent in several transcription factors. For
example, both CBP/p300 and p/CAF have been found to acetylate MyoD at a group of
closely spaced lysine residues (K99, K101, K102) adjacent to its bHLH domain,
resulting in increased DNA binding and transcriptional activation. (136-138). Acetylation
of p53 also occurs at a cluster of closely spaced, evolutionarily conserved lysines (129) as
does acetylation of c-Myb (139,140).
2.9 CBP Interacts Directly with E2A Proteins
2.9.1 Identification of E2A-CBP Interactive Domains
A particular requirement for AD1, the amino-terminal activation domain of E2A in E2Amediated transcriptional activation (10,12,141) as well as growth deregulation by
oncogenic E2A-fusion proteins (84,141) has been noted. In the LeBrun lab, an unbiased
affinity screen was performed to identify proteins that interact with this region of E2A.
The transcriptional co-activator CBP was identified as an AD1-interactive protein in this
screen (unpublished results).
The E2A-CBP interaction was interesting since a functional interaction between E2A and
CBP has been suggested in the literature. Several groups have shown enhanced E2Amediated transcriptional activation of target genes when E2A is co-transfected with CBP
(11,142,143). Furthermore, co-expression of E2A and p300 in NIH 3T3 fibroblast cells
enhances E2A-mediated transcription through the immunoglobulin heavy chain enhancer
30
(11). Subsequent to the identification of CBP as an AD1 interactive protein, the LeBrun
lab has examined the domains required for both E2A and CBP to mediate the interaction.
Activation domain 1 of E2A contains a phylogenetically conserved α-helical region
(amino acids 11-28) (10) and is required for interaction with the yeast co-activator
complex SAGA suggesting this region may mediate interactions with mammalian coactivators (12). An α-helical region within AD2 has also been identified but has no
homology to the helical region of AD1 (27). The α-helical regions of AD1 and to a lesser
extent, AD2 were found to contribute to the recruitment of CBP/p300 and p/CAF from
crude nuclear extracts and full transcriptional activation of a reporter gene by E2A 1-483
indicating a role for the E2A-CBP interaction in regulating E2A transcriptional activation
activity (13).
Mapping of the E2A-interactive domain on CBP determined that the CREB-binding
domain or KIX domain, is required and sufficient for the interaction with E2A (13). The
KIX domain has been well characterized and is known to mediate interactions with the
transcriptional activator domains of several proteins through interactions with LXXLL
motifs (28,144-147). In E2A, an LXXLL motif is found as an amino-terminal extension
of the LDFS motif (LXXLLDFS). The interaction between E2A and the KIX domain of
CBP was subsequently shown to be direct and involve the LXXLLDFS motif (13,14). In
fact, interaction between an E2A peptide containing this region of AD1 of E2A and the
KIX domain promotes the adoption of an α-helical structure by the E2A peptide
(14,148). Targeted amino acid substitution of the common leucine residue in the
31
LXXLLDFS motif, to alanine (L20A), impairs the interaction with CBP as well as the
adoption of a helical conformation due to binding (14). Since AD1 of E2A is required for
transcriptional activation (10,12,141) and growth deregulation by oncogenic E2A-fusion
proteins (84,141) it is reasonable to suspect the E2A-CBP interaction might be involved
in mediating the neoplastic functions of E2A-fusion proteins.
2.9.2 Functional Significance of the E2A-CBP Interaction for E2A-PBX1-mediated
Leukemogenesis
The E2A-PBX1 oncoprotein is capable of inducing the outgrowth of immortal, highly
proliferative myeloid progenitors from retrovirally transduced primary mouse bone
marrow (149). Abrogation of the E2A-CBP interaction by deletion of the AD1 α-helix
alone, or in combination with, the AD2 α-helix reduced cellular proliferation of
transduced cells (13). Furthermore, disruption of the E2A-CBP interaction by engineered
mutations of the AD1 α-helical region (e.g. L20A) in E2A-PBX1 abrogated the ability of
E2A-PBX1b to stimulate proliferation of primary hematopoietic cells retrovirally
transduced to express E2A-PBX1b demonstrating a critical role for the LXXLLDFS
motif in mediating growth deregulation by E2A-PBX1 (14).
In a whole animal model sub-lethally irradiated mice reconstituted with bone marrow
transduced with E2A-PBX1b-L20A did not develop an aggressive myeloproliferative
disease seen in animals reconstituted with E2A-PBX1b transduced bone marrow (14).
32
This result suggests a role for the LXXLLDFS motif and interaction with the CBP KIX
motif in mediating the oncogenic effects of E2A-PBX1 (13,14).
In summary, the interaction between AD1 of E2A and the KIX domain of CBP is direct
and required for E2A-PBX1-mediated oncogenesis. The E2A-PBX1-CBP interaction
could potentially contribute to leukemogenesis in several ways: First, E2A-mediated
recruitment of co-activators, such as CBP, to PBX1 defined target genes may promote
aberrant transcriptional activation. Second, in a DNA binding independent manner,
interaction between AD1 of E2A-PBX1 might sequester CBP, in a dominant-inhibitory
fashion, from wild-type E2A or other factors. Finally, the association between E2APBX1 and CBP might alter the enzymatic activity of CBP itself.
33
Chapter 3
Hypothesis and Research Objectives
The amino-terminal activation domain of E2A, AD1, is critical for transcriptional
activation by wild-type or chimeric E2A proteins (10,26) as well as growth de-regulation
and oncogenesis by E2A-PBX1 (13,83,84,141). This region mediates interactions with
the histone acetyltransferase co-activator proteins CBP/p300 and p/CAF (13). The
interaction between E2A-PBX1 and CBP/p300 is required for leukemia induction by
E2A-PBX1 (13,14). Therefore, the direct physical interaction between E2A proteins and
CBP/p300 has important functional consequences for both proteins. My research was
undertaken with the general objective of elucidating these consequences.
Hypothesis
The direct physical interaction between E2A transcription factors and co-activator
proteins CBP/p300 will result in post-translational modification of lysine residues within
E2A. These modifications will affect the transcriptional activation activity of E2A.
Furthermore, the interaction between E2A and CBP/p300 may affect the intrinsic
acetyltransferase activity of CBP/p300 proteins.
Research Objectives
1) Determine if the physical interaction between E2A and co-activator proteins
results in acetylation of E2A itself and identify the acetyltransferase enzyme
responsible.
34
2) Map the acetylated lysine residues within the E2A portion of E2A-PBX1
3) Determine if acetylation affects E2A-mediated protein-protein interactions
4) Determine the effect of E2A acetylation on the transcriptional regulatory function
of E2A
5) Determine if the physical interaction between E2A and CBP affects the
acetyltransferase activity of CBP and map the required domains on both proteins.
35
Chapter 4
Materials and Methods
4.1 Plasmids
Plasmids conferring bacterial expression of the glutathione-S-transferase (GST)-E2A
fusion proteins were generated by PCR amplification using a vector containing the full
length E2A-PBX1 cDNA and ligated into BamHI and EcoRI sites of the GEX-2T vector
(Amersham-Pharmacia Biotech) as described in (13). Site directed mutagenesis of lysine
residues was performed using the Transformer Site-Directed Mutagenesis kit (Clontech).
Amino acid substitutions were verified by sequencing.
Mammalian plasmids conferring expression of GAL4-E2A proteins were generated by
restriction digestion of the GST-E2A plasmids with EcoRI followed by creation of a
blunt end using Klenow and digestion with BamHI. The E2A insert DNA was ligated into
the CMV-GAL4 vector, digested with SmaI and BglII.
Plasmids conferring bacterial expression of the glutathione-S-transferase (GST) fusion
proteins GST-CBP-HAT, GST-PCAF-HAT, GST-p45 and GST-f(GATA-1) have been
described previously (150-153) and were generous gifts of Dr. Gerd Blobel ( Children’s
Hospital of Philadelphia, Philadelphia, Pennsylvania, USA). Mammalian expression
vectors conferring expression of full-length wild-type and mutant CBP proteins (i.e.
CMV5-CBP-WT-FLAG, CMV5-CBP-ΔKIX-FLAG, CMV5-CBP-ΔBROMO-FLAG and
CMV5-CBP-ΔHAT) were also generous gifts of Dr. Gerd Blobel.
36
The mammalian expression vector pCMV-FLAG-SUMO-1 was a generous gift of Dr. G.
Nucifora (154); pMT-35 c-JUN-HIS and pMT 123 HA-ubiquitin were generous gifts of
Dr. Dirk Bohmann (University of Rochester) (155,156).
4.2 Preparation of GST-fusion Proteins
Plasmid DNA was electroporated into competent BL-21 (DE3)pLysS or BL21CodonPlus-RP E.coli cells (Stratagene). Bacteria were grown in 2YT media
supplemented with ampicillin (100μg/ml) (BL21) or ampicillin (100μg/ml) and
chloramphenicol (50μg/ml) (BL21-RP). Protein was purified essentially as described in
the GST Gene Fusion System handbook (Amersham-Pharmacia Biotech 3rd edition,
Revison 2, 1997), dialyzed against Phosphate Buffered Saline (PBS) and stored at -20°C
in 50% glycerol (v/v).
Proteins used for in vitro HAT assays were dialyzed against BC100 Buffer (20mM TrisHCl pH 8.0, 100mM KCL, 0.5mM EDTA pH8.0, 20% glycerol, 0.5mM DTT, 0.5mM
PMSF) after elution, concentrated with Centricon spin columns (Millipore) and stored at
-80°C. Protein concentrations were determined by Coomassie brilliant blue staining of
SDS-PAGE gels by comparison with known amounts of bovine serum albumin (BSA).
37
4.3 Preparation of nuclear extracts
The pre-B acute lymphoblastic leukemia cell line RCH ACV associated with t(1;19) and
expressing endogenous E2A-PBX1 protein, was grown to confluency in 100mm diameter
tissue culture dishes in RPMI supplemented with 10% fetal bovine serum. Cells were
harvested and nuclear extracts prepared using the Dignam and Roeder method (157).
Briefly, the RCH ACV cells are pelleted and resuspended in a hypotonic buffer (Buffer
A, 10mM Hepes-KOH pH7.9, 1.5mM MgCl2, 10mM KCl, 0.5mM DTT, protease
inhibitors). The cell pellet is homogenized using a dounce homogenizer and checked for
the presence of nuclei. The nuclei are pelleted by centrifugation and resuspended in a
hypertonic buffer (Buffer B, 20mM Hepes-KOH pH7.9, 25% glycerol, 0.42M NaCl,
1.5mM MgCl2, 0.2mM EDTA pH8, protease inhibitors). The nuclei are homogenized and
the solution stirred on ice for at least one hour. The nuclear solution is centrifuged and
the supernatant containing nuclear proteins is dialysed for 5 hours at 4°C against Buffer
D (20mM Hepes-KOH pH7.9, 20% glycerol, 0.1M KCl, 0.2mM EDTA pH8, 0.5mM
DTT). Following dialysis the extract is centrifuged to remove proteins, including
histones, which have precipitated. The supernatant is aliquoted and stored at –80°C.
4.4 Pull-downs using nuclear extracts
5 to 20μg of GST-E2A fusion protein bound to glutathione sepharose (AmershamPharmacia Biotech) beads were incubated overnight at 4°C with 0.5 to 1mg of RCH ACV
nuclear extracts. Beads and retained proteins were washed in HEGN buffer (20mM
38
HEPES-KOH, pH 7.9, 0.1mM EDTA, pH 8.0, 10% glycerol, 0.1% NP4, 1mM DTT,
0.5mM PMSF) and analyzed by SDS-PAGE and immunoblotting.
4.5 Pull-downs using purified, recombinant CBP, p300 or p/CAF
GST-E2A 1-483 (2.5μg) was bound to glutathione sepharose and blocked in HEGN
buffer containing 1mg/ml Bovine serum albumin prior to incubation with 0.1pmol p300
or p/CAF.
GST-E2A 1-483 (5pmol) was bound to glutathione sepharose and blocked in HEGN
buffer containing 1mg/ml bovine serum albumin prior to incubation with 5pmol of CBP.
In both experiments the proteins were incubated together overnight at 4°C. Beads were
washed 3 times in HEGN buffer and retained proteins were analysed by SDS-PAGE and
immunoblotting.
4.6 In Vitro acetylation site mapping
0.4μg of enzyme (GST-CBP-HAT or GST-PCAF-HAT) and 4.0μg of GST fusion protein
are mixed in a final reaction volume of 30μl containing acetyltransferase (HAT) buffer
(50mM Tris-HCl, pH 8.0, 50mM NaCl, 10% glycerol, 2.5mM MgCl2, 10mM sodium
butyrate, 0.5mM dithiothretol (DTT), 0.5mM phenylmethylsulfonyl fluoride (PMSF))
(150) and 1μl 14C-acetyl-coEnzyme A (51.4 mCi/mmol, 0.02mCi/ml) (NEC313 Perkin
Elmer) Reactions were incubated at 30°C for 1-2 hours. Acetylation products were
39
analyzed by SDS-PAGE and visualized following fluorography of the gel using
En3Hance (NEF981 Perkin Elmer) and autoradiography. Acetylation levels were
determined by scintillation counting of acetylated bands or quantified using a Phosphor
screen and Phosphor Imager.
In reactions using purified, recombinant p300 or p/CAF, 0.1pmol of enzyme was
incubated with 5pmol of GST-E2A in HAT reaction buffer with and 1μl 14C-acetylcoEnzyme A for 2 hours at 30°C. Acetylation products were analyzed by SDS-PAGE and
visualized following fluorography of the gel using En3Hance and autoradiography.
Acetylation levels were quantified using a Phosphor screen and Phosphor Imager.
4.7 Pull-Down/Acetyltransferase reaction
5 to 20μg of GST-E2A fusion protein bound to glutathione sepharose (AmershamPharmacia Biotech) beads were incubated overnight at 4°C with 0.5 to 1mg of RCH ACV
nuclear extracts. Beads and retained proteins were washed three times in HEGN buffer
(20mM HEPES-KOH, pH 7.9, 0.1mM EDTA, pH 8.0, 10% glycerol, 0.1% NP40, 1mM
DTT, 0.5mM PMSF). Beads were washed once in 1X HAT buffer, resuspended in 30μl
HAT buffer plus 1μl 14C-acetyl-coEnzyme A and incubated at 30°C for 1-2 hours.
Products were analyzed by SDS-PAGE and viewed following fluorography of the gel
using En3Hance and autoradiography or are transferred to nitrocellulose and
immunoblotted.
40
Immunoblotting was performed using antibodies specific for E2A (sc-416 Santa Cruz) or
CBP (s-c7300 Santa Cruz).
4.8 Preparation of full-length CBP, p300 and p/CAF proteins
Plasmid conferring expression of full-length CBP proteins were transiently transfected
into SV293T cells, maintained in DMEM supplemented with 10% fetal bovine serum,
using the calcium phosphate method. Two days after transfection cells were harvested
and lysed in 50mM Tris pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100 with
protease inhibitors. Lysates were cleared by centrifugation and incubated with 20μl AntiFLAG M2 agarose (Sigma-Aldrich) per ml of lysates for 2 hours at 4°C. Beads were
washed 3 times in TBS and the FLAG-tagged CBP eluted using excess 3X-FLAG
peptide (200ng/μl). Proteins were aliquoted and stored at -80°C. The protein
concentration was determined by Coomassie brilliant blue staining of SDS-PAGE gels by
comparison with known amounts of bovine serum albumin.
Full-length HIS-tagged p300 and FLAG-tagged p/CAF proteins were produced by
baculovirus infection of the SF21 insect cell line (Generous gift of Dr. Roger Deeley,
Cancer Research Institute, Queen’s University, Kingston, Ontario). Baculovirus
supernatants for p/CAF and p300 and purification protocols were provided by Dr. Jeffrey
Dilworth (Ottawa Health Research Institute, Ottawa, Ontario) with permission from Dr.
Yoshihiro Nakatani (123) and Dr. W. Lee Kraus (158).
41
For HIS-tagged p300, cells were harvested 2 days after infection and resuspended in
homogenization buffer (10mM Tris-HCl, pH 7.5, 0.5M NaCl, 10% glycerol (v/v), 0.1%
NP40 (v/v), 15mM imidazole, 2mM β-mercaptoethanol, 2mM PMSF, 50μg/mL
aprotinin) Cells were lysed by homogenization and cleared by centrifugation. The lysate
was then incubated with nickel-NTA agarose (Qiagen) for 2 hours followed by four
washes of the matrix in wash buffer (10mM Tris-HCl, pH 7.5, 0.2M NaCl, 10% glycerol
(v/v), 0.2% NP40 (v/v), 15mM imidazole, 2mM β-mercaptoethanol, 2mM PMSF). The
p300 protein was eluted in elution buffer (10mM Tris-HCl, pH 7.5, 0.2M NaCl, 10%
glycerol (v/v), 0.1% NP40 (v/v), 250mM imidazole, 2mM β-mercaptoethanol, 2mM
PMSF), aliquoted and stored at -80°C. The protein concentration was determined by
Coomassie brilliant blue staining of SDS-PAGE gels by comparison with known amounts
of bovine serum albumin.
FLAG-tagged p/CAF, was purified from SF21 cells 2 days after infection. Cells were
washed twice in PBS and resuspended in 1X FLAG Buffer (20mM HEPES- KOH pH
7.6, 150mM KCl, 2mM MgCl2, 0.2mM EDTA, 10mM β-glycerophospahte, 15% glycerol
(v/v), 1mM DTT, 0.2mM PMSF). Cells were lysed by dounce homogenization and the
cellular debris was pelleted by centrifugation. Cellular extract was incubated with AntiFLAG M2 agarose with 0.2% NP40 for 2 hours. The extract/agarose mix was added to a
column, washed once with high salt FLAG buffer (0.6M KCl, 2mM DTT, 2mM PMSF,
0.2% NP-40) and once with low salt FLAG buffer (1X Flag buffer containing 1mM DTT,
0.3mM PMSF, 0.1% NP40). Proteins were eluted with 1X FLAG buffer containing
42
2mg/ml 3X-FLAG peptide and 1mM PMSF. Proteins were aliquotted and stored at 80°C. The protein concentration was determined by Coomassie brilliant blue staining of
SDS-PAGE gels by comparison with known amounts of bovine serum albumin.
4.9 Luciferase Assays
HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum. The
day before transfection 1.7 X105 cells/well were plated in 12 well plates. Cells were
transiently transfected by the calcium phosphate method. Transfection cocktails were
prepared using an 8:1 ratio of reporter to transactivator, total 6μg DNA per well (5.3μg
5X GAL4-luciferase reporter, 0.7μg GAL4 or GAL4-E2A 1-483 plasmids and 0.05μg
pRL-CMV a renilla luciferase-expressing plasmid (Gift of Chris Mueller, Queen’s
University, Ontario, Canada)). The cells were lysed 40 h later in passive lysis buffer
(Promega), and a portion of the lysates was analysed using the dual luciferase reporter
assay system (Promega) and an LB 96V Micro Lumat Plus Microplate Luminometer (EG
and G Berthold Ltd., Bundoora, Australia). Each luciferase value was normalized using
the corresponding renilla value as a measure of transfection efficiency. The mean value
from each triplicate experiment was considered as one data point and the results shown
are the average of at least three independent experiments.
4.10 Histone Acetyltransferase Gel Assays
Reactions using purified, recombinant p300 (0.1 pmol) was incubated with 5 pmol of
GST-E2A and 2.5μg unfractionated calf thymus histones in 1X HAT reaction buffer with
43
and 1μl 14C-acetyl-coEnzyme A for 2 hours at 30°C. Acetylation products were analyzed
by SDS-PAGE and visualized following fluorography of the gel using En3Hance and
autoradiography. Acetylation levels were quantified using a Phosphor screen and
Phosphor Imager.
4.11 Histone Acetyltransferase Filter Assays
Filter assays were performed as essentially as described (159-161). A typical reaction
contained 0.5 pmol of CBP protein and 5.0 pmol of GST or GST-E2A 1-483 in 25 μl
final volume of 1X reaction buffer (50mM Tris HCl, pH8, 10% Glycerol, 50mM NaCl,
12.5mM MgCl2, 10mM sodium butyrate, 0.5mM DTT, 0.5mM PMSF) (162). Enzyme
and E2A were incubated for 10 minutes at 4°C to allow interaction between E2A and
CBP and 5 minutes at 30°C to equilibrate the temperature. The HAT reaction was
induced by addition of 1.0μl 14C- acetyl-coenzyme A (60mCi/mmole) and 2.5μg
unfractionated calf thymus histones (Sigma-Aldrich, H9250) or nucleosomes. Reactions
were incubation at 30°C for 5 minutes prior to stopping the reaction by spotting onto P81
phosphocellulose filter discs (Whatman). Dried filters were wash twice for 5 minutes
each, in 50mM Na2CO3 pH 9.2, rinsed in acetone and thoroughly air-dried before liquid
scintillation counting.
4.12 Chloramphenicol Acetyltransferase Assays
44
U2OS cells and pcDNA3-GAL4-CBPHAT plasmids were gifts from Gerd Blobel
(Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA). Cells were
maintained in DMEM supplemented with 10% fetal bovine serum. The day before
transfection 1.5 X105 cells/well were plated in 12 well plates. Cells were transiently
transfected by the calcium phosphate method with mammalian expression and reporter
plasmids as described (163). Briefly 2μg of pcDNA3-GAL4-CBPHAT-CBP2 or
pcDNA3-GAL4-CBPHATΔ-CBP2 and 2μg of CMV-E2A, CMV-E2A-PBX1 or CMVPBX1 plasmids along with 2μg of the CAT reporter plasmid (5XGAL4-AdML-CAT) and
0.1μg pRL-CMV were used. The cells were harvested, resuspended in 100ul 25mM Tris,
pH 7.5 and lysed by three freeze-thaw cycles. A portion of the lysate (60μl) was analysed
for CAT activity using the FAST CAT Green (deoxy) Chloramphenicol Acetyltransferase
Assay Kit (Molecular Probes) and thin layer chromatography (TLC) on silica gel plates
following the manufacturers instructions. The chloramphenicol substrate in this kit has
been modified to incorporate a green fluorophor and contains only one potential
acetylation site resulting in only one acetylated species, thus the rate of acetylation is a
direct function of enzymatic activity. Using a Lichtox Research Imaging Platform the
TLC plates were excited with 470nm +/- 20nm light and emission at 520nm +/- 20nm
imaged with a Hamamatsu Orca Camera. Imaging was performed with the assistance of
Mr. Jeff Mewburn. The acetylated products were then quantified using Image Pro Plus
(Media Cybernetics) software and expressed relative to GAL4-CBPHAT-CBP2 alone. A
portion of the lysates (20μl) was also analysed using the dual luciferase reporter assay
system (Promega) and an LB 96V Micro Lumat Plus Microplate Luminometer (EG and
G Berthold Ltd., Bundoora, Australia). Each CAT value was normalized using the
45
corresponding renilla result as a measure of transfection efficiency. Each experiment was
performed in duplicate. Results shown represent a typical experiment.
4.13 Immunoblotting Antibodies
Following SDS-PAGE and electorphoretic transfer to a nitrocellulose membrane
(PROTRAN nitrocellulose membrane NBA085C, Perkin Elmer) membranes were
blocked of at least 1 hour in PBS containing 5% non-fat dried milk and 0.1% Tween 20.
Primary antibodies were incubated overnight at 4°C in PBS containing 0.1% Tween 20
and 3% dried milk. Membranes were washed in PBS containing 0.1% Tween 20 and
incubated with a secondary antibody conjugated to horseradish peroxidase (Jackson
ImmunoResearch Laboratories) for 1 hour. After washing, the secondary antibody was
detected using chemiluminescence, according to the manufacturer’s instructions (Western
Lightning Chemiluminsecent Reagent Plus, Perkin Elmer). The following primary
antibodies were used in this thesis. Anti-FLAG M2 (Sigma-Aldrich F-3165), anti-GAL4
(DBD) sc-577, anti-E2A (Yae) sc-416, anti-CBP (A-22) sc-369, anti HA (Y-11) sc-805,
anti-HIS (H-15) sc-803, anti-CBP (C-1) sc-7300, anti-p300 (C-20) sc-585 (Santa Cruz
Biotechnology).
46
Chapter 5
Acetylation Of Lysine 34 in E2A Proteins Contributes to
Transcriptional Activation
5.1 Contributions
Mutagenesis of K34Q and luciferase experiments shown in Figure 12 were performed by
Mr. Richard Bayly. GAL4-E2A constructs used in luciferase assays were sub-cloned
from existing GST-E2A vectors by Mr. Richard Bayly and Mr. Richard Casselman. Mr.
Bayly was responsible for preparation of RCH ACV nuclear extracts. Initial stocks of
purified, recombinant, full-length p300 and p/CAF were a generous gift of Dr. Jeffrey
Dilworth. Additional protein stocks were prepared by Mr. Bayly by infection of SF21
cells with p/CAF and p300 baculoviruses and subsequent purification of these
recombinant proteins.
5.2 Rationale
The LeBrun lab has demonstrated that the amino terminal two-thirds of E2A (amino
acids 1-483) can recruit the co-activator proteins CBP, p300 and p/CAF from nuclear
extract prepared from the t(1;19)-positive, acute lymphoblastic leukemia cell line RCH
ACV (13). The interaction between E2A and CBP was determined to involve α-helical
regions located within the transcriptional activation domains AD1 and AD2 of E2A and
the KIX domain of CBP. The consequences of the interaction between E2A and coactivator proteins on E2A function have not been fully described. This chapter will
47
describe experiments examining the effects of the interaction with CBP, p300 and p/CAF
on E2A.
5.3 Results
5.3.1 The Portion of E2A Included in E2A-PBX1 Interacts with Acetyltransferase
Proteins Capable of Acetylating Both Histones and E2A
A biochemical approach was employed to determine if the co-activator proteins recruited
by E2A retain intrinsic acetyl-transferase activity. Amino acids 1-483 of E2A were
expressed in bacteria as an in-frame fusion with glutathione-S-transferase (GST) and
purified on glutathione sepharose beads. GST-E2A 1-483 protein bound to beads was
incubated with crude nuclear extract to allow protein-protein interactions to occur. The
beads and associated proteins were then washed and transferred to acetyl-transferase
reaction buffer in the presence of unfractionated calf thymus histones and 14C-acetyl coenzyme A. The reactions were analyzed by SDS-PAGE and fluorography.
The GST-E2A 1-483 protein, but not GST, was capable of recruiting interacting proteins
that acetylated histones (Figure 4a). When the experiment was repeated in the absence of
histones and exposed longer the predominant band visualized after autoradiography
corresponded in size (~80 kDa) to GST-E2A 1-483 (Figure 4b). A large acetylated
species specific to the GST-E2A pull-down lane was also apparent well above the 175
kDa marker, indicating the presence of an unidentified E2A interactive protein of nuclear
extract origin. This protein was subsequently identified as CBP by an anti-CBP
48
immunoblot (Figure 4c). These results indicate that the portion of E2A contained within
the leukemogenic fusion protein E2A-PBX1 (i.e. E2A 1-483) can recruit proteins capable
of acetylating histones and E2A itself.
49
Figure 4: (a) E2A recruits histone acetyl-transferase activity from nuclear extracts.
GST or GST-E2A 1-483 fusion protein bound to glutathione-Sepharose beads were
incubated overnight with lymphoid nuclear extract derived from RCH ACV cells.
Retained proteins were subjected to an in vitro acetyltransferase (AT) assay in the
presence of purified histones and 14C-acetyl Co-enzyme A and then analyzed by SDSPAGE and autoradiography. (b) E2A is acetylated by the recruited histone
acetyltransferase activity. A similar experiment with omission of purified histones from
the reaction and a longer exposure of the gel shows acetylation of GST-E2A 1-483.
Acetylation of a large, unidentified protein of nuclear extract origin that migrates well
above 175 kDa is also evident, in additional to several faint bands that migrate faster than
GST-E2A 1-483. A least some of the latter could be truncation products related to GSTE2A 1-483. (c) A large acetylated E2A-interactive protein corresponds to CBP. AntiCBP immunoblotting identifies the large E2A-interactive protein as CBP.
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5.3.2 Acetylation of E2A Correlates with Recruitment of CBP
Our lab has reported that the interaction between E2A and CBP is direct and requires a
conserved α-helical region located within the amino terminal 28 residues of AD1 and to a
lesser extent involves an α-helical region located within AD2. Recruitment of p/CAF
from crude nuclear extracts by E2A also requires these domains (13). Experiments were
performed to determine if the same regions are required for recruitment of acetyltransferase (AT) activity and for acetylation of the E2A protein itself.
A series of GST-E2A fusions with amino- and carboxy-terminal deletions (Figure 5a)
were used as ligands in pull-down experiments performed with crude nuclear extracts.
GST-E2A, or engineered variants, and retained interactive proteins were subjected to
SDS-PAGE and immunoblotted with a monoclonal anti-CBP antibody (Figure 5b) or
transferred to acetyltransferase buffer in the presence of 14C acetyl-Co-enzyme A before
analysis by SDS-PAGE and fluorography (Figure 5c). Constructs able to pull-down CBP
(i.e. 1-483, 1-273, 1-220, 1-160) were also acetylated while those that could not recruit
CBP (i.e. 1-99, 29-273, 60-273, 100-273, 274-483) were not acetylated.
Amino acids 1-28 of E2A are required for the CBP interaction and consequent
acetylation of E2A even in the context of a relatively large portion of E2A (compare 1273 and 29-273, Figure 5 and (13)). This region of E2A comprises a phylogenetically
conserved α-helical region containing an LDFS (amino acids 20-23) motif required for
interaction with the SAGA co-activator complex and maximal E2A transcriptional
52
activity (10,12) and an LXXLL motif (amino acids 16-20; where X equals any amino
acid) (28,29), thought to be involved in mediating interaction with co-activators. These
results demonstrate that the conserved α-helical region of AD1, is required to recruit
acetyl-transferase activity capable of acetylating E2A. E2A amino acids 1-160 are
sufficient for CBP recruitment and contain four putative substrate lysine residues (Figure
5d). The correlation between CBP recruitment and E2A acetylation suggests that CBP
may be the responsible HAT enzyme.
53
Figure 5: Acetylation of E2A correlates with recruitment of CBP. (a) Schematic
indicating the domains of E2A-PBX1a and the segments of E2A expressed as aminoterminal fusions with GST. AD, activation domain; HD, homeodomain. (b) Mapping of
CBP-interactive elements within E2A. GST fusion proteins were bound to glutathione
sepharose and incubated with nuclear extracts in pull-down assays. Retained proteins
were washed and analysed by anti-CBP immunoblots (c) E2A fragments that retain CBP
from nuclear extracts also serve as substrates for acetylation. Pulldown assays were
followed by incubation of the retained proteins in acetyltransferase buffer in the presence
of 14C acetyl-CoA. The small arrow indicates an acetylated protein whose presence
correlates with E2A acetylation and whose large size is consistent with CBP/p300. *
indicates intact GST-E2A proteins.At least some smaller bands visible in the
autoradiograph and coomassie stained gels are truncation products related. (d) An Nterminal α-helical region of E2A is required for interaction with CBP (anti-CBP
immunoblot, upper image) and consequent acetylation of E2A 1-160 (autoradiograph,
lower image). The amino acid substitutions (L19R/F22R) were designed to disrupt the
E2A-CBP interaction.
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55
56
5.3.3 In Vitro Acetylation of E2A
The co-activator p/CAF co-purifies with CBP and possesses intrinsic AT activity (123)
that could also potentially acetylate E2A proteins. Experiments were performed to
determine whether recombinant CBP or p/CAF were capable of acetylating E2A. GST
fusion proteins expressing only the catalytic acetyl-transferase domains of CBP (GSTCBP-HAT, amino acids 1196-1718) or p/CAF (GST-p/CAF-HAT, amino acids 352-832)
were incubated with GST-E2A 1-483 in HAT reaction buffer in the presence of 14Cacetyl Co-enzyme A. The reactions were analysed by SDS-PAGE and fluorography. The
catalytic domain of p/CAF was capable of acetylating GST-E2A 1-483; GST-p45 served
as a positive control (Figure 6a). Although it readily acetylated GST-f(GATA-1), which
served as a positive control, the catalytic domain of CBP was unable to acetylate GSTE2A 1-483 (Figure 6b). Neither catalytic domain could acetylate GST alone, indicating
that both enzymes retained substrate specificity.
In order to investigate the possibility that acetylation of E2A by CBP/p300 requires a
full-length acetyltransferase, the HAT assays were repeated using recombinant, fulllength p/CAF and p300. Full-length p/CAF was capable of acetylating E2A, (Figure 6c)
consistent with the results using the isolated catalytic domain. Interestingly, full-length
p300 was capable of acetylating E2A, unlike the isolated CBP catalytic domain.
Quantification of acetylation levels by Phosphor Imager revealed that p300 acetylated
E2A at a level 2.54 times greater than p/CAF. When p/CAF and p300 were incubated
simultaneously with GST-E2A 1-483, acetylation of E2A appeared greater than with
either p300 or p/CAF alone. Quantification revealed greater than additive acetylation
57
Figure 6: Acetylation of E2A by purified CBP/p300 or p/CAF. (a) The isolated
catalytic domain of p/CAF acetylates amino acids 1-483 of E2A (lane 1) and the positive
controls p45 and GATA-1 (lanes 2 and 3, respectively). The auto-acetylated p/CAF
catalytic domain migrates as two bands, indicated by the arrows. In lane 1, full-length
GST-E2A 1-483 overlaps or is juxtaposed with the upper p/CAF-related band. However,
multiple GST-E2A-related truncation products are readily visible. * indicates p45, @
indicates GATA-1, arrows indicate auto-acetylated p/CAF. (b) The isolated catalytic
domain of CBP cannot acetylate recombinant E2A 1-483. The positive control GATA-1
is acetylated (lane 2). @ indicates GATA-1 (c) Both full-length recombinant p300 and
p/CAF acetylate E2A 1-483. Co-incubation of E2A with p300 and p/CAF results in
greater than additive acetylation of E2A (1.7 fold higher).
58
59
60
relative to that resulting from the individual AT enzymes, suggesting p300 and p/CAF
may co-operate to achieve maximal acetylation of E2A.
5.3.4 Both p300 and p/CAF Interact Directly with E2A
We have previously demonstrated a direct interaction between E2A and CBP/p300 (13).
p/CAF was identified due to its ability to interact with either CBP or p300 (123). The
p/CAF protein also interacts with E2A (13,143), however, the possibility exists that the
E2A-p/CAF interaction could be indirect and mediated by CBP/p300. To investigate this
possibility purified, recombinant, full-length FLAG-tagged p/CAF and HIS-tagged p300
were incubated alone or in combination with GST-E2A 1-483 or GST bound to
glutathione sepharose beads. Following pull-downs, proteins associated with the beads
were analyzed by SDS-PAGE and immunoblotting with antibodies directed against the
affinity tags present on p/CAF (FLAG) or p300 (HIS). GST-E2A 1-483, but not GST,
was able to pull-down p300 and p/CAF individually (Figure 7, lanes 6 and 7) or in
combination (lane 4). These results indicate that p/CAF, like CBP/p300, interacts
specifically and directly with E2A. Interestingly, co-incubation of p300 and p/CAF seems
to enhance the retention of p300 by E2A suggesting p/CAF may stabilize the interaction
between E2A and p300.
61
Figure 7: p/CAF interacts directly with E2A. GST-E2A-1-483 or GST were used in
pull-down experiments with purified recombinant p/CAF and p300, alone (lanes 6 and 7)
or in combination (lanes 4 and 5). Lanes 1,2, and 3 represent one-tenth input. Following
pull-downs, protein complexes bound to glutathione-sepharose were washed and
interactive proteins eluted from glutathione-sepharose with excess reduced glutathione.
All samples were analysed by SDS-PAGE and immunoblotting with antibodies directed
against the epitope tag present on p/CAF (FLAG) and p300 (HIS).
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63
5.3.5 Acetylation of E2A Promotes its Interaction with CBP
Acetylation of another member of the bHLH family, MyoD, results in increased affinity
for CBP/p300 (131). Acetylation of the c-MYB transcription factor, which like E2A
interacts with the KIX domain of CBP/p300, also increases the strength of its interaction
with CBP (139). Therefore the effect of E2A acetylation on its interaction with CBP was
tested. GST-E2A 1-483 was acetylated using recombinant GST-p/CAF-HAT prior to its
use as a ligand in a pull-down experiment with RCH ACV nuclear extracts. The amount
of CBP retained by acetylated versus non-acetylated E2A was determined by SDS-PAGE
and an anti-CBP immunoblot. Pre-acetylated E2A was able to pull down more CBP than
un-acetylated E2A. An anti-E2A immunoblot confirmed equivalent loading of GST-E2A
fusion protein (Figure 8a). This result indicates that acetylation of E2A 1-483 enhances
its ability to interact with CBP from nuclear extracts, at least under the assay conditions
used here.
In order to investigate this result further we examined the ability of GST-E2A 1-483, or
an engineered version of GST-E2A in which all 10 lysines within the E2A portion were
converted to arginine (lysine-less), to pull-down full-length recombinant p300. The GST
proteins were bound to glutathione-sepharose beads prior to the addition of p300 and 14C
acetyl-CoA to the reactions to allow acetylation. The amount of p300 retained was
analysed by SDS-PAGE and immunoblotting. The results indicate that both wild-type
and lysine-less E2A pull-down similar amounts of p300 (Figure 8b) under the conditions
of this experiment.
64
Figure 8: Acetylation of E2A promotes its interaction with CBP/p300 from nuclear
extracts. (a) Pre-acetylation of E2A by p/CAF enhances its recruitment of CBP/p300
from nuclear extracts (upper image). Acetyl-coenzyme A was omitted from parallel
reactions as a negative control. Re-probing the same blot with anti-E2A indicates
equivalent loading of the E2A-fusion protein (lower image). (b) E2A acetylation does not
enhance its interaction with full-length, recombinant p300. Bacterially expressed and
purified wild-type (WT) or lysine-less (LL) GST-E2A 1-483 immobilized on glutathione
sepharose beads were incubated with baculovirus-expressed wild-type HIS-tagged p300
under acetyl-transferase assay reaction conditions. Bead-protein complexes were washed
and analyzed by SDS-PAGE and anti-p300 immunoblotting. Lane 1 represents one-tenth
input.
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66
This result, using purified p300, is inconsistent with our previous finding showing
enhanced ability of acetylated E2A to recruit CBP from nuclear extracts. The discordance
between the results in Figures 8a and 8b could reflect the involvement of additional,
unidentified nuclear proteins in stabilizing the E2A-CBP/p300 interaction. p/CAF
represents a potential candidate as it enhanced retention of p300 by E2A using purified
proteins (Figure 7). Alternatively, the ability of lysine-less E2A to recruit equivalent
amounts of p300, compared to wildtype E2A, may reflect the supra-physiological
amounts of p300 used in the assay. In addition, the lack of any apparent difference
between the amount of p300 recruited by acetylatable (i.e. wildtype) verses nonacetylatable (i.e. lysine-less) E2A may also reflect a situation on which prior acetylation
of E2A by p/CAF is required to mediate the enhanced interaction between E2A and p300.
5.3.6 Mapping of Acetylated Lysines
E2A residues 1-483 contain ten lysines residues. Each of these is phylogenetically
conserved and represents a potential substrate for acetylation (Figure 9). The aminoterminal 160 amino acid of E2A includes AD1, contains four lysines (K14, K34, K101,
K144), is capable of recruiting CBP and HAT activity from nuclear extracts and is itself,
acetylated (Figure 5). A weak consensus site for acetylation of non-histone proteins by
CBP/p300 and p/CAF, GKXXP (X denotes any amino acid), has been identified
(129,164). Lysine 34 is located within such a consensus (GKGRP) just carboxy-terminal
of the putative α-helical region (amino acids 11-28) that is required for interaction with
CBP (24). Therefore, K34 represents an attractive candidate for acetylation. Furthermore,
67
Figure 9: Schematic indicating the location and phylogentic conservation of lysine
residues in the E2A portion of E2A-PBX1. The sequence alignment of E-proteins
shows tight phylogenetic conservation lysine residues and of the GKXXP consensus.
Numbers represent amino acid position of lysines in human E2A.
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69
the location of this residue within AD1 suggests that its acetylation status may affect the
transcriptional function of this domain. Site directed mutagenesis was used to replace
lysine (K) residues with arginine (R) as arginine mimics an unacetylated, positivelycharged lysine.
In vitro HAT reactions using the catalytic domain of p/CAF as the HAT protein and
GST-E2A 1-160 fusion proteins as substrates were performed. The resulting acetylation
of E2A was quantified by scintillation counting of excised E2A bands. A K34R
substitution decreased (24.8% relative to wild-type), but did not abrogate, acetylation
relative to wild-type 1-160, indicating that GST-p/CAF-HAT acetylates lysine 34 and at
least one other residue within this portion of E2A (Figure 10, lane 2). The three
remaining lysine residues (K14, K101, K144) were substituted to arginine in combination
with K34R and tested in the acetylation assay. As expected, substitution of all four
lysines essentially abrogated detectable acetylation (lane 6). Substitution of lysine 101
(partial consensus, GK) (lane 4) or lysine 144 (lane 5) in combination with K34R also
essentially abrogated acetylation, indicating that these residues are also acetylated. In
contrast, conversion of lysine 14 to arginine in combination with K34R did not result in
decreased acetylation relative to K34R in isolation (33.4% versus 24.8%, lanes 3 and 4).
These results suggest that, at least under the conditions of this assay, the catalytic domain
of p/CAF acetylates lysines 34, 101, and 144, but not lysine 14, of E2A.
70
Figure 10: The catalytic domain of recombinant p/CAF acetylates lysines 34, 101
and 144 of E2A. In vitro acetylation of E2A 1-160 or lysine to arginine substitution
mutants by the recombinant p/CAF catalytic domain. Closed arrows, p/CAF catalytic
domain; open arrows, GST-E2A 1-160 proteins. * indicates the positive control p45.
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Additional lysine to arginine substitution mutants were generated to examine acetylation
of the carboxy-terminal lysines in E2A 1-483 in the context of K to R substitution of the
4 amino-terminal lysines (i.e., K14R, K34R, K101R and K144R). The isolated catalytic
domain of p/CAF could not be used to examine acetylation of the six carboxy-terminal
lysines in GST-E2A 1-483 as it co-migrates with GST-E2A and is auto-acetylated.
Therefore, the in vitro acetylation assays were performed using full-length, recombinant
FLAG-tagged p300 and the reactions subjected to SDS-PAGE and fluorography. The gel
was then exposed to a Phosphor screen in order to quantify the level of acetylation of the
various mutants relative to that of the wild-type E2A, using a Phosphor Imager.
Substitution of the 4 amino-terminal lysine residues reduced acetylation of E2A 1-483 by
p300 to 54% of wild-type level, indicating that p300 also acetylates at least a subset of
these lysine residues as well as additional, more carboxy-terminal residues. Additional
substitution of a cluster of three lysines residues (K171, K172, K175) further reduced
acetylation (25% of wild-type E2A), indicating that full-length p300 acetylates at least
one of these (Figure 11a, lane 6). A construct containing only K171, K172 and K175
(lane 6) as potential substrates for acetylation was acetylated at levels similar to the
construct with substitution of the amino-terminal four lysines only (lane 3) (40% versus
54%, respectively), suggesting that acetylation by p300 of at least one of these residues
accounts for most of the acetylation beyond that related to K34, K101 and K144. Lysine
334 falls within a partial GKXXP consensus, GK, and also appears to be acetylated in
this assay as mutation of this residue further decreased acetylation of the E2A protein
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(compare lanes 4 and 5) to levels barely above a lysine-less E2A construct, which served
as the negative control (lane 7).
The HAT activity recruited by E2A from crude nuclear extracts was examined to
determine if it acetylates similar lysine residues as purified, full-length p300. GST-E2A
1-483 proteins were used as ligands in a pull-down experiment using nuclear extracts
prepared from RCH ACV cells. The pull-downs were followed by incubation of the
complex under acetylation reactions conditions and the resulting acetylation evaluated by
SDS-PAGE and fluorography. This experiment (Figure 11b) revealed an identical
pattern of acetylated residues compared to the previous experiment using purified
recombinant p300 (Figure 11a). Of the six carboxy-terminal lysines examined, the E2Ainteractive HAT complex appears to acetylate at least one of the lysines in the cluster (i.e.
K171, K172, K175; lane 6) as well as K334 (compare lanes 4 and 5) but not K204. Due
to low amount of lysine-less protein (lane 7) we were unable to determine a relative
acetylation value. However, this protein is not acetylated in all previous experiments. A
large acetylated band corresponding in size to CBP/p300 consistently appears in all GSTE2A pull downs suggesting CBP/p300 may be the HAT protein responsible for
acetylating E2A in this assay. Importantly, CBP/p300 is retained in equivalent quantities
by the various lysine substitution mutants, indicating that differential acetylation of the
mutant E2A proteins could not be accounted for by effects on the affinity of the
interaction with CBP/p300
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Figure 11: Recombinant p300 and the co-activator complex recruited from nuclear
extracts acetylate identical lysine residues within E2A amino acids 161-483. (a) Fulllength p300 was incubated with GST-E2A 1-483 containing various lysine to arginine
substitutions in acetyl-transferase reaction buffer in the presence of 14C acetyl-Co A.
Reactions were analysed by SDS-PAGE and fluorography. (b) GST-E2A 1-483
substitution mutants were used as ligands in pull-down experiments with nuclear extracts.
Immobilized GST-E2A 1-483 and interactive proteins were incubated with 14C acetyl-Co
A in acetyl-transferase reaction buffer and analysed by SDS-PAGE and fluorography.
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5.3.7 Transcriptional Activation by AD1 Involves Acetylation of K34
Acetylation of transcription factors is known to have a variety of effects, including
alteration of transcriptional activation. Several studies have indicated enhanced
transcriptional activation activity by E2A on co-transfection with co-activators, including
CBP, p300 and p/CAF (11,142,143). In order to investigate whether acetylation of E2A
amino acids 1-483 may alter its transcriptional function, plasmids conferring mammalian
expression of the lysine substitution mutants, as fusions with a heterologous DNA
binding domain derived from the yeast transcription factor GAL4, were constructed.
These plasmids were co-transfected into HeLa cells with a reporter plasmid that confers
expression of firefly luciferase regulated by five tandem GAL4 DNA-binding sites. All
results were normalized for transfection efficiency using a co-transfected plasmid that
confers constitutive expression of renilla luciferase. In the graph, the results are expressed
relative to that obtained using wild-type GAL4-E2A 1-483 and represent an average of
three independent experiments. Substitution of lysine 34 (K34R) significantly reduced
transcriptional activation relative to that observed using wild-type E2A (74.7%) (Figure
12). Substitution of K14, K101, K144 or K144 to arginine in combination with K34R
had little additional effect on transcriptional activation by E2A compared to K34R alone,
(69.9%, 68.1% and 72% respectively versus 74.7%) Substitution of the amino-terminal
three (K14R, K34R, K101R) lysines only slightly decreased E2A transcriptional
activation compared to the double mutants. However, additional substitution of K144 (i.e.
K14R, K34R, K101R, K144R) further decreased transactivation to 54.7% of wild-type
suggesting post-translational modification of K34, K101 and K144 may be involved in
regulating E2A activity.
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The role of the more carboxy-terminal 6 lysine residues was investigated in the context of
lysine to arginine mutation of the four amino-terminal lysines (K14R, K34R, K101R,
K144R). An E2A protein with additional substitution of lysines 171, 172 and 175 further
reduced the transcriptional activation compared to the quadruple mutant (43.2% versus
54.7%, respectively,) suggesting that at least one of these lysines plays a role in E2A
function. Additional substitution of lysine 334 in combination with K171R, K172R and
K175R did not significantly effect E2A transcriptional activation compared to K171R,
K172R and K175R (44.7% versus 43.2%, respectively) suggesting that modifications at
K334 do not contribute to transcriptional activation by E2A. An E2A protein containing
only lysines 171,172 and 175 as candidate substrates for modification was not
significantly different from the quadruple mutant (52% versus 54.7%) providing
additional evidence that lysine modification of at least one of these residues, and not
K204, K334 or K392, may play a role in modulating E2A function.
Several observations implicate acetylation, as opposed to other lysine modification, of
K34 in the transcriptional function of AD1. Arginine substitution at this site substantially
impaired transcriptional activation. In addition, this residue is found within a GKXXP
consensus motif for acetylation of non-histone proteins and is located adjacent to a
helical region of E2A that we have shown to interact directly with the KIX domain CBP
(13). We now demonstrate that this residue is a substrate for acetylation. Additional
experiments were undertaken to show that acetylation, and not another lysine
modification of K34 is the relevant modification.
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Figure 12: Post-translational modification of lysine 34 is involved in transcriptional
activation by E2A. (a) HeLa cells were co-transfected with wild-type or lysine to
arginine substitution mutants of E2A fused to the DNA-binding domain of GAL4 along
with a reporter plasmid that confers expression of firefly luciferase regulated by tandem
GAL4 binding sites. The role of lysine residues in E2A-mediated transcriptional
activation was examined using lysine substitution mutants. The plasmid pRL-CMV,
which confers constitutive expression of renilla luciferase was also co-transfected and
was used as a measure of transfection efficiency. Transfections were performed in
replicates of four and the results represent the average from at least three independent
experiments. (b) Anti-E2A immunoblot of whole cell lysates from a typical experiment
shows expression of all E2A mutants.
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5.3.8 Role for Acetylation of Lysine 34 in the Transcriptional Function of
Activation Domain 1
Lysine residues are also substrates for several post-translational modifications besides
acetylation, including ubiquitination and sumoylation. Whereas the side chain of arginine
is positively charged at neutral pH, mimicking an acetylated lysine, the side chain of
glutamine is uncharged, mimicking acetylated lysine. Therefore lysine 34 was substituted
by site directed mutagenesis, to glutamine (K34Q) in the context of GAL4-E2A 1-483
and tested for transcriptional activation activity. The K34Q mutant reconstituted E2Amediated transcriptional activation to at least levels associated with the wild-type protein
(Figure 12) further supporting a role for acetylation of K34 in the transcriptional function
of AD1.
The E2A transcription factors E12 and E47 possess a relatively short half-life in vivo and
have been shown to be poly-ubiquitinated downstream of Notch-1 signaling (64,66).
This results in accelerated degradation through the 26S proteasome. E12 and E47 are also
known to interact with the SUMO conjugating enzyme UBC-9 through a domain that
spans the fusion point with PBX1 in E2A fusion proteins (63-65). Ubiquitination and
sumoylation of the oncogenic portion of E2A (i.e. amino acids 1-483) has not been
examined.
Additional experiments were performed to examine whether E2A 1-483 may serve as a
substrate for ubiquitination or sumoylation. Plasmids conferring constitutive expression
of HIS-tagged E2A 1-483 or c-JUN (positive control) were transiently co-transfected into
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SV293T cells with a plasmid conferring expression of hemaglutinin (HA) tagged
ubiquitin. The HIS-tagged proteins were affinity purified from whole cell lysates on
nickel NTA agarose and eluted proteins were evaluated by SDS-PAGE and
immunoblotting with an anti-HA antibody to detect ubiquitinated E2A or c-JUN. Since
substrates may be poly- or mono-ubiquitinated at multiple lysine residues, a positive
reaction will result in ubiquitinated proteins of increasing size, producing a smear on the
anti-HA immunoblot. Although c-JUN was ubiquitinated as expected, E2A 1-483
protein was not ubiquitinated in this assay, suggesting that this portion of E2A is not a
substrate for ubiquitination (Figure 13a).
Similar experiments were performed to examine sumoylation of E2A 1-483. HIS-tagged
JUN, wild-type and lysine-less E2A 1-483 were co-transfected with an expression vector
for FLAG tagged-SUMO. Whole cell lysates were prepared and HIS-tagged proteins
purified and analysed as described for ubiquitin experiments. An anti-FLAG immunoblot
shows only the c-JUN positive control to be sumoylated; neither the wild-type E2A 1-483
nor the lysine-less (LL) negative control were sumoylated (Figure 13b).
Together, these results suggest that acetylation and not ubiquitination or sumoylation of
lysine residues within E2A 1-483 is the key post-translational modification involved in
regulating E2A-mediated transcriptional activation activity.
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Figure 13: The oncogenic portion of E2A is not a substrate for ubiquitination or
sumoylation. (a) SV293T cell were transiently transfected with wild-type, HIS-tagged
E2A 1-483, a lysine-less (LL) E2A mutant or HIS-tagged c-JUN (positive control), with
or without HA-tagged ubiquitin. HIS-tagged proteins were affinity purified from whole
cell lysates using nickel NTA agarose and subjected to SDS-PAGE and immunoblotting.
Top panel, anti-HA, detects ubiquitinated proteins; bottom panel, anti-E2A. (b)
Transfections and protein purification were performed as described for (a) except FLAGtagged SUMO was co-transfected in place of HA-ubiquitin. Top panel, anti-FLAG,
detects sumoylated proteins; bottom panel, anti-E2A. Large white circle in the c-Jun +
FLAG-SUMO lane is a result of excessive signal consuming the luminol reagent. The
lysine-less E2A mutant serves as a useful negative control in this experiment.
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5.4 Discussion
Over the past several years the list of acetylated transcription factors has grown
considerably. Initially thought to be restricted to histones and involved in modulation of
chromatin conformation, protein acetylation is now know to also modulate a variety of
functions associated with transcription factors, including: DNA binding, sub-cellular
localization, protein-protein interactions and transcriptional activation (15). Recently, the
LeBrun lab has described a direct interaction between AD1 of E2A and the KIX domain
of CBP (13,148). The E2A-CBP interaction is required for E2A-PBX mediated growth
deregulation in tissue culture models (13) and leukemogenesis in vivo (14). This chapter
describes an investigation of one of the downstream consequences of the interaction
between E2A and the co-activators CBP, p300 and p/CAF, namely, acetylation of E2A
itself.
In the work described here, I have used pull-downs to demonstrate the portion of E2A
found in the oncogenic fusion protein E2A-PBX1, i.e. E2A amino acids 1-483, recruits
histone acetyltransferase activity able to acetylate histones and E2A itself from the
human ALL cell line RCH ACV. Furthermore, recruitment of HAT activity correlates
with recruitment of the co-activators CBP/p300 and p/CAF, suggesting that one of these
proteins may be the HAT protein responsible for acetylation of E2A. In fact, all three coactivators efficiently acetylate E2A 1-483.
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The result showing a direct interaction between E2A and p/CAF is novel and raises the
possibility that p/CAF may modulate the function of E2A activity. Interestingly, using
purified proteins, p/CAF was able to enhance the amount of p300 retained by E2A. In
addition, p300 and p/CAF seem to co-operate to achieve maximal E2A acetylation.
Together, these results suggest p/CAF may be functioning to stabilize the interaction
between E2A and p300 resulting in greater acetylation of E2A. These results also point to
p/CAF as a potential candidate for the unknown nuclear factor that enhances the ability of
acetylated E2A to retain CBP from nuclear extracts.
Enhanced recruitment of CBP/p300 by acetylated E2A could have several functional
implications. For instance, the enhanced localization of CBP/p300 to promoters regulated
by acetylated E2A or E2A-PBX1 genes would likely result in increased acetylation of
nucleosomal histones and other chromatin-associated proteins. Acetylation also creates
docking sites for bromodomain-containing proteins resulting in recruitment of additional
factors required for transcription. In the case of E2A-PBX1, this would result in aberrant
expression of PBX1 defined target genes involved in leukemogenesis. In a DNA-binding
independent manner, the enhanced recruitment of CBP/p300 could result in a dominantnegative effect on other transcription factors that require CBP/p300 for proper function.
This study maps, for the first time, several acetylated lysines within the oncogenic
portion of E2A, (i.e. amino acids 1-483) using recombinant CBP/p300 and p/CAF as well
as the HAT complex recruited from nuclear extracts. Three amino-terminal lysines (K34,
K101 and K144), in addition to the more carboxy-terminal K334 and at least one of the
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lysines in a cluster (i.e. K171, K172 and K175) are substrates for acetylation.
Interestingly, acetylation of E2A by CBP/p300 required more that an isolated catalytic
domain. Discrepancies have been noted between the ability of the isolated catalytic
domain of CBP/p300, relative to the full-length protein, to mediate acetylation of
substrates. MyoD is a bHLH family member that is involved in promoting muscle cell
terminal differentiation and is acetylated by p/CAF (137). Polesskaya et al demonstrated
that full-length CBP/p300 was capable of acetylating MyoD both in vivo and in vitro
(136). A later study, however, showed that the isolated catalytic domain of CBP/p300
was unable to acetylate MyoD (165). MyoD has been shown to interact with the C/H3
domain of CBP/p300 (166) and, like E2A, interacts with the KIX domain of CBP/p300
(167), these domains are truncated or absent when using an isolated catalytic domain.
Polesskaya et al demonstrated that acetylation of MyoD, by p300, requires a direct
interaction between the proteins (138). Therefore, the lack of E2A acetylation by the
isolated catalytic domain of CBP is likely due to the loss of key protein-protein
interaction domains.
Bradney et al have described acetylation of the E2A splice variant E2-5 in vitro and in
vivo by CBP/p300 and p/CAF (143). E2-5 lacks amino acids 1-99 (i.e. AD1) but contains
the E47 bHLH domains. In this study, Bradney et al showed that E2-5 co-elutes from
nuclear extracts with CBP/p300 and p/CAF in high molecular weight complexes.
However, since E2-5 lacks AD1 and the LXXLLDFS motif required for interaction with
the KIX domain of CBP (13,14,148) it is reasonable to speculate that the E2A-CBP
interactions seen in this study must be mediated by other E2A domains or additional
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proteins. The bHLH domain, for example has been shown to interact with CBP/p300 (11)
or perhaps the α-helical region of AD2 (13).
Consistent with previous studies (11,142) Bradney et al demonstrate that transcriptional
activation activity by E2-5 is increased by co-transfection of CBP/p300 or p/CAF(143).
However, this study did not examine the mechanism of enhanced E2A-mediated
transcriptional activation. Since E2-5 lacks amino acids 1-99 of E2A it does not contain
lysine 34. The location of K34 within AD1 suggested to us that post-translational
modifications at this site may play a role in regulating transcriptional activation by E2A
proteins. Mimicking an unacetylated state, by arginine substitution, substantially
decreased E2A mediated transcription of a reporter gene while substitution to glutamine,
mimicking the uncharged, acetylated state restores and perhaps enhances E2A activity
supporting the role of acetylation in mediating E2A transcriptional activation.
Furthermore, Mr. Bayly, in the LeBrun lab, has demonstrated in vivo acetylation of K34
using co-immunoprecipitations. An anti-acetyl-lysine antibody immunoprecipitated far
less E2A 1-483 with K34R or K34Q substitutions than wild-type E2A 1-483, from cells
co-transfected with CBP and E2A 1-483 expression vectors (unpublished results). This
result indicates that lysine 34 is a substrate for acetylation by CBP/p300 or p/CAF in cells
and confirms the in vitro result showing acetylation at this residue by the catalytic
domain of p/CAF.
In an attempt to rule out the involvement of other lysine post-translation modifications in
mediating E2A transcriptional activation I examined potential ubiquitination and
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sumoylation of E2A 1-483. However, I was unable to demonstrate ubiquitination or
sumoylation of E2A 1-483 in spite of the fact that E12 and E47 proteins have been
demonstrated to be ubiquitinated (66). My inability to demonstrate ubiquitination of E2A
1-483 could reflect the fact that most of the bipartite binding site for UBC9, required for
proteasomal degradation of E2A, is missing (63,64). Interestingly, the two chimeric E2A
oncoproteins, E2A-PBX1 and E2A-HLF, exclude the exon that encodes this degradation
domain (65). Alternatively, Notch-1 signals required for E2A phosphorylation and
subsequent interaction with the E3 ubiquitin ligase SCFSkp2 (66,69) were not induced in
the cell culture system used here.
Acetylation at the lysine cluster (K171, K172, K175) accounts for the majority of
acetylation amongst the carboxy-terminal six lysine residues. Interestingly, lysine to
arginine substitution of these residues also significantly decreased E2A-mediated
transcriptional activation, suggesting a role for acetylation at K171, 172 and K175 in
E2A driven transcription. The amino acid sequence at this lysine cluster (KKVRK)
represents a potential nuclear localization site (NLS) (loose consensus, K(K/R)X(K/R),
where X equals any amino acid) (168), suggesting that acetylation of these residues could
alter the sub-cellular localization of E2A proteins.
Recently, acetylation of the Max transcription factor at three lysine residues within its
nuclear localization signal (NLS) has been demonstrated and seems to result in
localization of the protein to the cytoplasm. Compartmentalization of Max to the
cytoplasm inhibits its ability to suppress c-Myc activated transcription (169). Therefore,
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the increased nuclear retention of E2A seen by Bradney et al, when co-transfected with
CBP/p300 or p/CAF (143), might be explained by acetylation of lysines within this NLS.
In the same manner, enhanced concentration of E2A in the nucleus might be partially
responsible for increased transcriptional activation by E2A when co-transfected with
CBP/p300 or p/CAF (143).
Several examples exist in the literature of enhanced transcriptional activation by a
transcription factor following acetylation. However, the mechanism of enhancement
seems to involve increased affinity of DNA (129,131,139,140). In the reporter assay used
in the current study, DNA-binding of E2A 1-483 is mediated by the GAL4 DNA-binding
domain and not endogenous bHLH or the PBX1-derived homeodomain, suggesting
another mechanism for regulation E2A transcriptional activation. In the case of the
muscle specific bHLH protein MyoD, the increased transcriptional activation by
acetylated MyoD has been suggested to be a result of the enhanced affinity of CBP/p300,
due to an acetylation-dependent interaction with the bromodomain of CBP/p300 (131). It
would be interesting to investigate the possibility of acetylated E2A interacting with the
bromodomains of CBP/p300 and p/CAF.
The carboxy-terminus of E2A (i.e. the portion not included in E2A-PBX1, containing the
bHLH domain) contains 12 (E47) or 13 (E12) additional lysine residues. The portion of
PBX1 included in E2A-PBX1 contains 15 lysines. In both cases several of the lysines are
located within domains that mediate dimerization with other proteins or the respective
DNA-binding domains. Post-translational modification of these lysine residues could
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potentially have affects on DNA binding of normal or oncogenic E2A proteins. In
addition, protein-protein interactions mediated by these regions could be affected by
acetylation. Therefore, investigation of the acetylation status of these lysines should be
pursued in the future to examine the functional consequences of post-translational
modification, specifically acetylation, on E2A function.
In summary, the discovery that the oncogenic portion of E2A (i.e. amino acids 1-483) can
mediate direct interactions with the transcriptional co-activators CBP/p300 (13) and
p/CAF (Figure 7, this thesis) resulting in acetylation of E2A itself is novel. E2A is
acetylated at multiple sites and acetylation appears to play a role in regulating E2Amediated transcriptional activation activity. Acetylation of E2A results in enhanced
retention of CBP/p300, in a manner that requires additional proteins, possibly p/CAF.
One might envision a model in which E2A recruitment of CBP/p300 and p/CAF results
in acetylation of E2A itself, stabilization of the complex followed by recruitment of
additional co-activators, ATP-dependent remodeling complexes and the transcriptional
machinery culminating in enhanced transcriptional activation of genes required for tissue
specific differentiation (normal E2A proteins) or oncogenesis (E2A-PBX1).
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Chapter 6
E2A Enhances the Acetyl-transferase Activity of CBP
6.1 Contributions
Preparation of small oligonucleosomes (SONs) from HeLa cells was performed by Mr.
Richard Bayly. Initial stocks of purified, recombinant, full-length p300 were a generous
gift of Dr. Jeffrey Dilworth. Additional protein stocks were prepared by Mr. Bayly by
infection of SF21 cells with p300 baculovirus and subsequent purification of the
recombinant protein.
6.2 Rationale
The E2A-CBP interaction is critical for E2A-PBX1-mediated leukemogenesis (14). In
addition, acetylation of E2A at several conserved lysines, including one located within
AD1, plays a role in transcriptional activation activity by E2A. An important
consequence of transcription factor-mediated recruitment of co-activators, such as
CBP/p300 and p/CAF, to gene promoters is acetylation of lysine residues located within
the amino-terminal tails of nucleosomal histones, affecting the interaction between
histones and DNA. Acetylated histones are generally found at transcriptionally active
loci. Twist is a bHLH protein implicated in inhibition of differentiation of multiple cell
lineages (170,170-176). Twist interacts directly with the HAT domains of p300 and
p/CAF in vitro and in vivo (173,177) and completely abrogates acetylation of histones as
well as auto-acetylation of the co-activators (177). Inhibition of HAT activity by Twist
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does not require its bHLH domain suggesting dimerization with other bHLH proteins is
not required for inhibition transactivation (177). Since E2A is also a bHLH transcription
factor that interacts with co-activators we decided to investigate the possibility that the
interaction between E2A and CBP may affect the catalytic activity of CBP.
6.3 Results
6.3.1 E2A Proteins Enhance in vitro Acetylation of Histones by CBP/p300
In order to investigate the possibility that interaction with E2A proteins are capable of
modulating the catalytic activity of CBP/p300, amino acids 1-483 of E2A were expressed
as an in-frame fusion with glutathione-S-transferase (GST) and purified on glutathione
sepharose beads. GST E2A 1-483, or GST alone, was incubated with full-length p300 in
the presence of free histones and 14C-acetyl co-enzyme A. Full-length, recombinant p300
was expressed by baculovirus infection of SF21 insect cells and affinity purification
using nickel NTA agarose. Samples were subjected to SDS-PAGE and the resulting gel
was Coomassie-stained and photographed prior to fluorography. After several weeks on
film the gel was transferred to a Phosphor screen and acetylation levels of histones
quantified using a Phosphor Imager. Values were normalized according to the quantity of
histone protein present in each lane, as determined by densitometry of the Coomassie
stained gel.
GST-E2A 1-483, but not unfused GST, was capable of enhancing the acetylation of
histones by approximately two-fold (Figure 14a) by p300. The enhancement of HAT
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activity did not require acetylation of E2A, as a lysine-less E2A mutant was also capable
of enhancing p300 HAT activity (2.7 fold increase), note the absence of a band
corresponding to acetylated E2A in this lane.
A faster method of examining the effects of E2A proteins on HAT activity that does not
require lengthy exposure to film, would allow multiple replicates to be performed and
that would more readily allow kinetic parameters to be investigated was sought out. A
filter-binding HAT assay has been described. This entails incubating a HAT enzyme,
histones as a substrate, and 14C-acetyl-CoA in reaction buffer for a period of time prior to
stopping the reaction by spotting onto phosphocellulose filters (159-161). These are then
washed to remove unincorporated label and the labeled (i.e., acetylated) proteins are
quantified by liquid scintillation counting of the filter.
In order to examine the effect of E2A on the rate of CBP-mediated acetylation of
histones, a time course experiment was performed. Full-length, FLAG-tagged CBP
(CBP-WT) was immuno-affinity purified from whole cell lysates of transiently
transfected SV293T cells on M2 anti-FLAG agarose beads. GST-E2A 1-483 was
incubated with CBP-WT in a 10:1 molar ratio (0.2 pmol/μl E2A, 0.02 pmol/μl CBP) for
10 minutes prior to addition of histones and 14C-acetyl-CoA. The results presented in
Figure 15 represents the mean of two independent experiments. The linear portion of the
graph was determined using linear regression analysis and the slope of the line represents
reaction rate. Incubation of CBP with histones yielded a reaction rate of 2.3X10-3μM/s.
Addition of E2A to the reaction mixture increased the rate to 5.3X10-3μM/s. Therefore,
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the addition of E2A results in a 2.3-fold increase in the reaction rate, a value that is
similar to that found using full-length p300 in the gel-based assay (Figure 14a).
Extension of the lines to the axis reveals that they do not intersect zero on the graph. This
is likely due to the fast rate of histone acetylation by CBP and technical limitations of the
filter assay itself, at very short time points. A reaction time of 5 minutes was used in all
subsequent filter assays. Together these results demonstrate for the first time that E2A is
capable of enhancing the intrinsic HAT activity of CBP/p300.
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Figure 14: E2A enhances the histone acetyltransferase activity of p300. (a) HAT
assays were performed using full-length, HIS-tagged p300 produced by baculovirus
infection of SF21 cells and affinity purification. Acetylation levels were quantified and
normalized against the quantity of histone protein in each lane. WT, wild-type; lysineless, an engineered E2A mutant with arginine substitutions at all 10 E2A lysine residues;
L20A, leucine to alanine substitution at E2A residue 20; Δ397-405, deletion of an αhelical region within E2A activation domain 2. (b) Increasing the amount of E2A from
5pmol to 15pmol does not further enhance p300 HAT activity.
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Figure 15: Time course experiment showing that E2A enhances the catalytic activity
of CBP approximately two-fold. CBP was incubated in reaction buffer in the presence
of 14C-acetyl-co enzyme A and histones for different time periods. At the completion of
the reaction, the solution was spotted onto a phosphocellulose filter which were then
washed to remove unincorportated label. Acetylated proteins bound to the filter were
quantified by scintillation counting. The graph shows the concentration of acetylated
histones (μM) versus time (seconds) by full-length, recombinant CBP in the absence
(dark circles) or presence (light circles) of a 10-fold molar excess of E2A 1-483. The
addition of E2A to the reaction increases the reaction rate from 2.3X10-3 μM/sec to
5.3X10-3 μM/sec, a 2.3 fold increase. The experiment was performed twice and error bars
indicate standard deviation.
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6.3.2 Mapping of E2A Domains Required to Increase the HAT Activity of CBP
We next set out to identify the domains required, in both proteins, for E2A-mediated
enhancement of CBP/p300 histone acetylation. The LeBrun lab has previously identified
a direct interaction between an α-helical region within AD1 of E2A and the KIX domain
of CBP (13,148). Deletion or mutation of key residues within AD1 dramatically impairs
the CBP (i.e. KIX) interaction. An α-helical region within AD2 also contributes to the
interaction and is required for maximal transcriptional activation by E2A (13). The role
of these α-helical domains in enhancement of CBP HAT activity was investigated.
The filter-based HAT assay was performed using full-length GST-E2A 1-483 or GSTE2A 1-483 proteins with targeted deletions of the α-helical regions within AD1 and
AD2. The results shown in Figure 16 are displayed relative to those obtained using fulllength CBP alone. Targeted deletion of the AD1 α-helix (Δ16-23) did not abrogate the
ability of E2A to enhance CBP HAT activity (1.4 fold versus 1.9 fold). Similarly,
deletion of the AD2 α-helical region (Δ 397-405) had little effect (1.5 fold versus 1.9
fold). Deletion of both α-helical regions did not significantly alter E2A-induced
enhancement of HAT activity (1.7 fold versus 1.9 fold). These results suggest that
protein-protein interactions mediated by the α-helical domains are not required for the
effect.
Further supporting the idea that the E2A-KIX interaction is not required for enhancement
of CBP/p300 HAT activity a gel based assay shows similar results. Deletion or mutation
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of the α-helical regions of E2A had no effect on the ability of E2A to enhance p300 HAT
activity (Figure 14). Together, these results suggest that the α-helical regions and by
implication the KIX interaction, is dispensable for the E2A-medaited stimulation of CBP
HAT activity.
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Figure 16: The α-helical domains within AD1 and AD2 of E2A are dispensable for
enhancement of CBP histone acetylation. HAT assays were performed using fulllength, recombinant CBP and GST-E2A 1-483 proteins. Δ16-23 and Δ397-405, deletions
of an α-helical regions within E2A activation domains 1 and 2. Error bars indicate
standard deviation calculated from the results of 5 filters counted for each reaction.
105
106
6.3.3 The KIX- and Bromo-domains are Dispensable for E2A-induced Increase of
CBP HAT activity
We next wanted to investigate the requirement of the well-characterized KIX interaction
in mediating the E2A-dependent enhancement of CBP catalytic activity. Full-length,
FLAG-tagged CBP proteins or mutant versions with deletion of the entire KIX domain
(amino acids 588-667, CBP-ΔKIX), most of the BROMO domain (Δ1107-1171, CBPΔBROMO) or a small region within the HAT domain (Δ1458-1475, CBP-ΔHAT) were
expressed in SV293T cells by transient transfection and immuno-affinity purified using
M2 anti-FLAG agarose beads for use in the HAT assay. The results shown in Figure 17a
are expressed relative to that obtained using CBP-WT without E2A. As previously
demonstrated (Figures 14, 15 and 16), addition of GST-E2A 1-483 increases the HAT
activity of CBP (1.9 fold). The CBP-ΔBROMO protein has somewhat lower HAT
activity compared to CBP-WT. However, the addition of E2A to the reaction results in
increased HAT activity compared to CBP-ΔBROMO alone (1.6 fold), a response similar
to that obtained using wild-type CBP. Deletion of the KIX domain has no effect on either
the ability of CBP to acetylate histones in the absence of E2A, or the ability of E2A to
enhance HAT activity (1.7 fold versus CBP-ΔKIX alone). As expected, the CBP-ΔHAT
mutant has markedly reduced HAT in the absence of E2A that is not augmented on
addition of E2A to the reaction. Together, these results indicate that the E2A-KIX
interaction and the bromodomain are dispensable in the enhancement of CBP HAT
activity.
107
The isolated catalytic domain of CBP (amino acids 1196-1718) fused in frame to GST
was used to further investigate the possibility that an interaction between E2A and the
HAT domain may be required to mediated enhanced CBP acetylation of histones. This
region contains the C/H2, HAT and most of the C/H3 domains of CBP. Co-incubation of
GST-CBP-HAT with E2A in the filter assay resulted in only a very small increase in
histone acetylation compared to GST-CBP-HAT alone (1.2 +/- 0.08 versus 1.0 +/- 0.05)
(Figure 17b). This result suggests that E2A interacts with a domain outside the isolated
HAT domain to mediate enhancement of HAT.
Previous mapping studies that identified the direct interaction between AD1 of E2A and
the KIX domain of CBP used small CBP domains as individual GST-fusion proteins (13).
Therefore, it remains possible that E2A could interact with additional CBP domains in
the context of full-length CBP. Pull-down experiments using GST-E2A 1-483 and fulllength, FLAG-tagged CBP proteins, expressed by transient transfection and immunoaffinity purification were performed to investigate this possibility. Retained proteins were
analysed by SDS-PAGE and anti-FLAG immunoblots. As expected, E2A was able to
recruit significant amounts of wild-type, full length CBP (Figure 17c). Deletion of the
entire KIX domain (amino acids 588-667) abrogated the interaction with E2A. Deletion
of most of the BROMO domain (amino acids 1107-1171) or a small region of the HAT
domain (amino acids 1458-1475) reduced but did not abrogate the interaction with E2A
1-483. These experiments confirm that the KIX domain is required to mediate a direct
interaction with E2A in the context of full-length CBP. The results also suggest that the
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BROMO and HAT domains of CBP may play a role in mediating the interaction with
E2A.
It is interesting that despite the inability of CBP-ΔKIX to interact with E2A in pull-down
assays it is still able to respond to E2A in the filter assay. It is possible that a lower
affinity interaction between E2A and CBP-ΔKIX is responsible for mediating the
interaction (and the enhanced HAT activity) in the filter assay in the absence of the KIX
domain. Reciprocally, the residual recruitment of CBP-ΔBROMO and CBP-ΔHAT in the
pull-downs is likely mediated by the KIX domain. The ability of CBP-ΔBROMO to
respond to E2A in the HAT filter assay reflects the ability of this protein to interact with
E2A through the KIX or other CBP domains.
109
Figure 17: The KIX and BROMO domains of CBP are dispensable for enhancement
of HAT activity by E2A. (a) HAT filter assays were performed using full-length,
recombinant CBP or CBP mutants containing deletion of the entire KIX domain (ΔKIX),
most of the bromodomain (ΔBROMO) or a small segment of the HAT domain (ΔHAT).
Error bars indicate standard deviation calculated from the results of 5 filters counted for
each reaction. (b) E2A only slightly enhances the HAT activity of an isolated CBP
catalytic domain. HAT assays were performed using the isolated catalytic domain of
CBP (GST-CBP-HAT) and GST-E2A 1-483. Error bars indicate standard deviation
calculated from the results of 5 filters counted for each reaction. (c) The BROMO and
HAT domains contribute to the interaction with E2A. GST-E2A-1-483 was used in pulldown experiments with purified recombinant full-length wild-type or deletion mutants of
CBP. Following the pull downs, protein complexes bound to glutathione-sepharose
beads were analysed by SDS-PAGE and immunoblotting with antibodies directed against
the affinity tag present on CBP (FLAG). An anti-E2A immunoblot was performed as a
loading control.
110
111
112
6.3.4 E2A does not enhance CBP Acetylation of Nucleosomes in vitro
The results demonstrating enhanced histone acetylation by CBP/p300 when incubated
with E2A were obtained using free histones purified from calf thymus. These are not
associated with DNA, therefore the lysine substrates are not in their normal cellular
configuration. Small oligonucleosomes (SONs) purified from HeLa cell nuclear pellets
represent a more biologically relevant substrate. Histone H1 depleted SONs were
prepared by Mr. Richard Bayly following the method described by Côté et al (178).
Briefly, large amounts of HeLa cells are grown and the nuclei are purified. Nuclear
pellets are lysed and the chromatin digested with micrococcal nuclease. Following
digestion, the sample is applied to a sepharose column and fractions collected. The
fractions containing short oligonucleosomes (four core histones only, determined by
absorbance at 260nM and SDS-PAGE) are pooled and quantified against known amounts
of free calf thymus histones on a Coomassie stained gel.
HAT assays were performed using full-length CBP, GST-E2A 1-483 and SONs. An
equivalent amount of SON derived histones, compared to free histones used in previous
experiments (0.2μg/μl) were used for the HAT assays. Acetylation of the SONs by CBP
was approximately 3 to 4 fold lower compared to acetylation of free histone by the same
amount of enzyme. Increasing the reaction time from 5 minutes to 30 minutes had no
effect on acetylation rates (not shown). Addition of E2A to the reactions did not enhance
the low level of CBP SON acetylation and the increased reaction time resulted in greater
E2A acetylation that accounts for any apparent increase in SON acetylation (Figure 18).
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Figure 18: E2A is unable to enhance CBP-mediated acetylation of nucleosomes in
vitro. HAT assays were performed using full-length, recombinant CBP and small
oligonucleosomes purified from HeLa cell nuclei. An equivalent amount of nucleosomal
histones was used as compared to free histones used in previous experiments. The HAT
reaction time was increased form 5 minutes to 30 minutes. A control reaction containing
CBP and E2A but lacking nucleosomes was performed and resulted in significant E2A
acetylation. This value was subtracted from the reaction containing CBP, E2A and
nucleosomes, to account for the contribution from acetylated E2A. Error bars indicate
standard deviation calculated from the results of 5 filters counted for each reaction.
114
115
The low SON acetylation rate could be accounted for by the fact that the histones are
structured in chromatin and may therefore be less accessible than free histone for
acetylation. Since E2A proteins must bind to chromatinized DNA in order to promote
gene expression, enhancement of CBP HAT activity by E2A may require a stable
interaction with chromatin or DNA. We sought out an in vivo assay to address this
possibility.
6.3.5 E2A Enhances CBP Catalytic Activity in vivo
Martinez-Balbas et al have established that the intrinsic acetyl-transferase activity of
CBP can stimulate transcription of a reporter gene when tethered to a promoter (163). In
this system, a segment of CBP including the HAT domain (amino acids 1099-1877) is
expressed as an in frame fusion with the DNA binding domain of GAL4 (Figure 19a) in
cells co-transfected with a reporter plasmid consisting of five GAL4 binding sites
upstream of the adenoviral major-late (AdML) promoter and the chloramphenicol
acetyltransferase (CAT) coding region (Figure 19a). A GAL4-CBP fusion (GAL4CBPHAT-CBP2) but not a catalytically dead mutant is able to activate expression of the
CAT reporter gene in the osteosarcoma cell line, U2-OS (163). Evidence exists to show
that transfected plasmid DNA does get rapidly chromatinized (179-181). This system will
allow us to investigate if E2A is able to enhance CBP-mediated histone acetylation on a
chromatinized template in vivo.
Plasmids conferring expression of GAL4-CBP and various E2A proteins were cotransfected into U2-OS cells with the AdML-CAT reporter. All values were corrected for
116
transfection efficiency using a co-transfected plasmid that confers constitutive expression
of renilla luciferase. The level of CAT expression was assayed using the FAST-CAT
deoxy-Green chloramphenicol kit (Molecular Probes). The chloramphenicol substrate in
this kit has been modified to incorporate a green fluorophor and contains only one
potential acetylation site. Therefore the rate of acetylation is a direct function of
enzymatic activity.
Whole cell lysates were incubated with the labeled chloramphenicol and the reactions
products resolved by thin layer chromatography (TLC) to separate acetylated from
unmodified substrates (Figure 19b). The resulting plates were excited with 470 nm +/20 nm light, emission at 520 nm +/- 20nm was imaged and fluorescent spots quantified
using Image Pro Plus software. The results presented in Figure 19 are typical of those
obtained in two independent experiments and are expressed relative to GAL4-CBPHATCBP2 alone. Co-transfection of GAL4-CBPHAT-CBP2 with E2A-PBX1 dramatically
increased CAT expression (12.6 fold) (Figure 19c). Full length E2A (E47) was also able
to enhance CBP-HAT dependent transcriptional activation (8.9 fold) as was E2A 1-483
(10.1 fold, data not shown) while neither PBX1a nor PBX1b was able to stimulate CBPHAT dependent transcriptional activation. Therefore, these results indicate the E2A
portion of the oncogenic E2A-PBX1 protein is responsible for mediating enhanced CBP
activity in vivo. In addition, the results demonstrate that E2A is able to enhance CBP
acetylation of chromatin in vivo. The results also confirm that the E2A-KIX interaction is
not required for E2A-mediated enhancement of CBP catalytic activity as this domain is
not present in the GAL4-CBP fusions.
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Figure 19: The E2A portion of E2A-PBX1 mediates enhanced acetyltransferasedependent transcriptional activation by CBP in vivo. (a) Schematic representation of
CBP and the GAL4-CBP Fusions used in the CAT reporter Assay. Modified from
reference 162. (b) E2A enhances CBP HAT activity in vivo. E2A and PBX1 proteins
were co-transfected with the HAT domain of CBP fused the GAL4 DNA, in U2OS cells,
along with a CAT reporter plasmid. The plasmid pRL-CMV, which confers constitutive
expression of renilla luciferase was also co-transfected and was used as a measure of
transfection efficiency. CAT assays were performed on whole cell lysates as described
for the Fast CAT Green deoxy-Chloramphenicol Acetyltransferase kit (Molecular
Probes). Fluorescent TLC plates were imaged and (c) quantified using Image ProPlus
software. All TLC values were corrected for transfection efficiency. Transfections were
performed in duplicate and error bars represent standard deviations. The values obtained
using GAL4-CBPHATΔ-CBP2 without or with co-transfected E2A, E2A-PBX1 or PBX1
are not significantly above zero. Error bars for all GAL4-CBPHATΔ-CBP2 transfections
overlap and cross zero suggesting that these are not significantly different from each
other.
118
119
120
6.4 Discussion
Transcriptional co-activators are intimately involved in regulation of chromatin structure,
assembly and gene transcription. The co-activators CBP, p300 and p/CAF possess
intrinsic acetyltransferase activity responsible for acetylation of lysine residues in core
histone proteins (114,123,125) and acetylation of histones is highly correlated with gene
expression (92,93). Since co-activators lack DNA binding elements, sequence specific
DNA binding transcription factors must first recruit them to gene promoters prior to
acetylation of chromatin (87,89).
We demonstrate here that E47 and the portion of E2A found within the oncogenic fusion
protein E2A-PBX1 (i.e. E2A 1-483) are able to enhance the histone acetyltransferase
activity of CBP/p300 using both in vitro and in vivo assays. This finding is novel and
represents a potential mechanism for regulation of target gene expression for normal and
oncogenic E2A proteins. While the ability of E2A to enhance CBP/p300 catalytic activity
is novel it is not unprecedented for a transcription factor to modulate HAT activity of coactivators. Several other transcription factors that interact with CBP/p300 and p/CAF
have also been shown to inhibit or enhance catalytic activity. For example, The Early Bcell Factor (EBF) collaborates with E47 in regulating early B-cell development (182184). Unlike MyoD and E2A proteins, EBF does not require the HAT activity of
CBP/p300 to stimulate transcription of its target genes (185). However, EBF does bind to
CBP/p300 within the HAT domain and inhibit acetylation (185) suggesting it may
function to sequester CBP/p300 from other transcription factors.
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The Epstein Barr Virus (EBV) immediate early protein Zta is a member of the basic
zipper (b-zip) family that interacts with CBP at its C/H3 domain. The interaction with
CBP enhances transcriptional activation by Zta and promotes reactivation of latent EBV
(186). Reciprocally, Zta stimulates HAT activity of CBP in a manner that requires the
transactivation and DNA binding domains of Zta. Two additional b-zip family members,
NF-E2 and C/EBPα, also stimulate CBP HAT activity of nucleosomal histones
suggesting, these b-zip proteins stimulate HAT activity by directing CBP to nucleosomes
(187,188).
The examples above suggest that transcription factor mediated enhancement or inhibition
of HAT activity requires a direct interaction with the HAT protein. A direct interaction
between AD1 of E2A and the KIX domain of CBP has been described (13,148).
However, I demonstrate here that the E2A-KIX interaction is dispensable for E2Ainduced stimulation of HAT activity both in vitro and in vivo. I provide evidence that the
BROMO and HAT domains of CBP contribute to the interaction with E2A. However, the
ability of E2A to enhance the catalytic HAT activity of CBP in vitro requires a domain
outside the region containing intrinsic HAT activity (Figure 17b). The results from the in
vivo CAT assays point to the BROMO, CH3 or TAZ domains as candidates for further
investigation.
Although the mechanism by which E2A and other transcription factors influence the
HAT activity has not been fully elucidated, it is unlikely that E2A enhances the catalytic
activity of CBP/p300 by an E2A-histone effect since E2A-mediated stimulation of
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histone acetylation could not be further augmented by a three-fold increase in the amount
of E2A added to the HAT reaction (Figure 14b). The E2A-mediated enhancement of
CBP HAT activity may be due to induction of conformational changes that alter
enzymatic activity or possibly affect interaction and/or accessibility of histones or other
proteins.
I also demonstrate that acetylation of E2A itself is not required for enhancement of p300
HAT activity as a lysine-less E2A was equally capable of mediating the effect. This
result suggests that acetylation of E2A is important for mediating other effects, perhaps
recruitment of additional factors through acetyl-lysine/bromodomain interactions.
In summary, the results presented in this chapter suggest a model of E2A-mediated
transcriptional regulation in which wild-type and oncogenic E2A-fusion proteins enhance
expression of target genes by altering the catalytic HAT activity of the co-activators
CBP/p300 to induce gene expression.
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Chapter 7
General Discussion and Future Directions
The co-activator proteins CBP and p300 are ubiquitously expressed and are intimately
involved in regulating gene expression from many promoters (189,190). While the
majority of the experiments described in this thesis used CBP, full-length p300 was used
as the HAT enzyme in a few experiments. These proteins are highly homologous and are
often used interchangeably in in vitro assays (113,115) however, in vivo they likely act
differently.
In mouse models, homozygous knockout of either CBP or p300 is embryonic lethal. The
homozygous knockouts display similar phenotypes and defects suggesting nonoverlapping functions of the two proteins (191-193). Alternatively, the total level of CBP
and p300 may be critical for proper development. In support of this model, mice
expressing only one copy of each of the CBP and p300 genes (double heterozygotes) are
also embryonic lethal (191). In humans, haplo-insufficiency of CBP and less frequently
p300, results in Rubenstein-Taybi syndrome (RTS), a congenital disease characterized by
mental retardation and congenital malformations in addition to a propensity for
malignancies (194). In fact loss of HAT activity may be sufficient to cause RTS (195).
Both p300 and CBP gene loci are involved in non-random chromosomal translocations
associated with acute myeloid leukemia (AML) resulting in expression of chimeric oncoproteins. CBP, for example, is fused to MOZ (monocyte leukemia zinc finger protein).
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MOZ is, itself, a HAT protein. MLL (mixed lineage leukemia protein) is a
methyltransferase (MT) protein and is involved in translocations with CBP and less
frequently, p300. In all cases, the portion of CBP/p300 retained in the fusion proteins
includes the bromodomain, HAT domain and carboxy terminal residues (reviewed in
(189)). The nature of the proteins involved in these translocations suggests mis-targeting
of the HAT and MT activities may play a role in leukemogenesis (196).
The E2A locus is involved in at least two non-random chromosomal translocations
associated with acute lymphoblastic leukemia. In both cases the translocation results in
expression of chimeric oncoproteins that contain the transcriptional activation domains
for E2A fused in frame to DNA binding elements derived from the translocation partner.
Importantly, deletion of transcriptional activation domain one (AD1) from E2A-PBX1
abrogates growth deregulation and neoplastic transformation (83,84,141) suggesting
protein-protein interactions mediated by AD1 are important for E2A-PBX1-mediated
leukemogenesis (84).
Recently Dr. LeBrun’s lab demonstrated a direct interaction between a conserved motif
in an α-helical region of AD1 of E2A and the KIX domain of the transcriptional coactivator CBP. Mutations that disrupt the E2A-CBP interaction (13,148) also abrogate
E2A-PBX1 mediated induction of proliferation in primary hematopoietic cells (13) and
leukemogenesis in lethally irradiated mice transplanted with primary bone marrow
transduced to express E2A-PBX1 (14). These results suggest the E2A-CBP interaction is
important for the function of normal and oncogenic E2A proteins. However, the
125
mechanism by which the interaction functions to regulate gene expression remains
unclear. The experiments described in this thesis were undertaken to investigate the
functional consequences, for both proteins, of the physical interaction between E2A and
CBP.
The experimental findings discussed in this thesis provide significant insight into the
mechanisms involved in regulating the transcriptional activity of wild-type and oncogenic
E2A proteins. Primarily, several acetylated lysine residues within E2A have been
identified and determined to play a role in regulation the transcriptional activation of
gene expression by E2A. Acetylation of E2A also appears to enhance the interaction
between E2A and the co-activator CBP.
The demonstration of a direct interaction between E2A and a second co-activator, p/CAF,
is novel and provides evidence that more than one co-activator is involved in regulating
E2A function. In particular, p/CAF appears to be the protein responsible for mediating
the enhanced interaction between CBP/p300 and E2A, in addition to co-operating with
p300 to maximally acetylate E2A. Together these results underscore the need to further
characterize the interaction between E2A and p/CAF, at structural and functional levels.
Perhaps the most interesting finding of this thesis is the identification of a novel
mechanism of E2A-mediated regulation of transcription, namely enhancement of the
intrinsic HAT activity of CBP/p300 both in vitro and in vivo. Surprisingly, the effect is
independent of the E2A-KIX interaction previously described in our lab (13,148) and
126
suggests E2A interacts with CBP at additional domains. My results suggest several
candidates including the BROMO, C/H3 or TAZ domains of CBP as potential interactive
partners for E2A in mediating increased HAT activity.
The finding that E2A-mediated enhancement of CBP HAT activity is independent of
E2A acetylation is interesting. We have recently demonstrated that retroviral transduction
on primary bone marrow cells with E2A-PBX1 containing arginine substitutions in all 10
of the E2A-derived lysine residues had no effect on in vitro immortalization, proliferation
or extended clonogenic potential, compared to normal E2A-PBX1. The lethal
myeloproliferative disease developed by irradiated mice transplantation with the
transduced cells was only slightly less aggressive with lysine-substituted E2A-PBX1
(LeBrun Lab, unpublished results). Since acetylation of E2A-derived lysines is not
required for E2A-PBX1-mediated oncogenesis, and E2A-PBX1 is capable of enhancing
HAT activity in the in vivo system, this newly identified activity of E2A proteins, i.e.
stimulation of CBP/p300 HAT activity, potentially plays a role in oncogenesis, by
misdirecting CBP HAT activity to promoters of genes required for leukemogenesis.
Alternatively, E2A-PBX1 can induce proliferation of cells in vitro (83,84,141) and
induce lymphoid tumours in mice (141) independent of DNA binding. Both these
functions require AD1, and by implication, interaction with CBP, suggesting E2A might
exert gain of function effects on CBP that could be responsible for some leukemogenic
properties.
127
Several lines of investigation remain to fully elucidate the downstream consequences of
the interaction between E2A and co-activators. These include but are not limited to:
1) Are lysines located within the PBX1 portion of E2A-PBX1 or the carboxyterminus of E12 or E47 acetylated?
2) What role does acetylation of these residues play in mediating the function of
oncogenic E2A proteins? Acetylation of lysine residues within domains required for
DNA binding or dimerization domains could potentially affect protein-protein
interactions and DNA binding affinity.
3) Does the direct interaction between E2A and p/CAF also result in enhanced HAT
activity? While I demonstrated a direct interaction between E2A and p/CAF, the
domains required to mediate the direct interaction have not been identified and the affect
of the interaction of p/CAF activity was not examined.
4) What is the order of events at endogenous promoters? MyoD interacts with and is
acetylated by both p/CAF and p300 (11,131,136-138). Using an in vitro transcription
system it has recently been described that transactivation at a muscle specific promoter
requires a specific sequence of events. MyoD/E47 heterodimers recruit p300 to the
promoter resulting in acetylation of histones 3 and 4. Histone acetylation recruits p/CAF
to the promoter where it acetylates MyoD (197). A similar system could be used to
128
investigate the sequence of events and roles of CBP/p300 and p/CAF in E2A-dependent
transcriptional activation at endogenous naked or nucleosomal promoters.
5) Is an ATP-dependent chromatin remodeling complex recruited as a result of the
E2A-CBP interaction? Acetylation of lysine residues within histone tails and nonhistone proteins generates recognition sites for bromodomains found in remodeling
complexes. Identification of additional proteins required for mediating E2A
transcriptional activation would provide additional insight into the mechanism
oncogenesis by E2A-PBX1.
In summary, the results presented in this thesis suggest a model of E2A-mediated
transcriptional regulation in which wild-type and oncogenic E2A-fusion proteins enhance
the local concentration of CBP to promoter elements, resulting in acetylation of E2A
itself and stabilization of the E2A-CBP interaction. This interaction results in
enhancement of CBP-HAT activity, likely due to an allosteric change, acetylation of
histones and recruitment of the transcriptional machinery to induce target gene
expression. Enhancement of CBP/p300 HAT activity by oncogenic E2A-PBX1 proteins
in vivo, suggests that some of its leukemia-promoting effects may be due to E2A-induced
gain of function effects on CBP/p300 and might play a role in the DNA-bindingindependent induction of proliferation.
129
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