Download Chromatin Modifications

yes no Was this document useful for you?
   Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Document related concepts

Gene nomenclature wikipedia, lookup

History of genetic engineering wikipedia, lookup

X-inactivation wikipedia, lookup

Minimal genome wikipedia, lookup

Vectors in gene therapy wikipedia, lookup

Short interspersed nuclear elements (SINEs) wikipedia, lookup

Biology and consumer behaviour wikipedia, lookup

Genome (book) wikipedia, lookup

Non-coding DNA wikipedia, lookup

Gene desert wikipedia, lookup

Point mutation wikipedia, lookup

Behavioral epigenetics wikipedia, lookup

Epigenetics of cocaine addiction wikipedia, lookup

Genome evolution wikipedia, lookup

Genomic imprinting wikipedia, lookup

RNA-Seq wikipedia, lookup

Microevolution wikipedia, lookup

Gene expression programming wikipedia, lookup

Site-specific recombinase technology wikipedia, lookup

Ridge (biology) wikipedia, lookup

Gene wikipedia, lookup

NEDD9 wikipedia, lookup

Gene expression profiling wikipedia, lookup

Artificial gene synthesis wikipedia, lookup

Transcription factor wikipedia, lookup

Cancer epigenetics wikipedia, lookup

Epigenetics of depression wikipedia, lookup

Designer baby wikipedia, lookup

Long non-coding RNA wikipedia, lookup

Epigenetics wikipedia, lookup

Epitranscriptome wikipedia, lookup

Therapeutic gene modulation wikipedia, lookup

Primary transcript wikipedia, lookup

Epigenetics of diabetes Type 2 wikipedia, lookup

Epigenetics in stem-cell differentiation wikipedia, lookup

Polycomb Group Proteins and Cancer wikipedia, lookup

Epigenomics wikipedia, lookup

Epigenetics of human development wikipedia, lookup

Epigenetics of neurodegenerative diseases wikipedia, lookup

Nutriepigenomics wikipedia, lookup

Nucleosome wikipedia, lookup

Histone acetyltransferase wikipedia, lookup

Epigenetics in learning and memory wikipedia, lookup

Vered Fishbain
Reading Group in Computational Molecular Biology
Some Definitions…
Chromatin is the complex of DNA and proteins found
inside the nuclei of eukaryotic cells.
Nucleosomes are the fundamental repeating subunits of
all eukaryotic chromatin. They are made up of DNA and
protein core, which is the histone core.
The histone core is composed by two copies of the
following set of proteins, called histones:
H2A, H2B, H3 and H4.
147 bp in each nucleosome.
Heterochromatin is condensed chromatin, includes
inactive genes and untranscribed regions (like the
Euchromatin is non-condensed chromatin, includes active
and repressed genes.
The Histone Core
Chromatin Modifications
Chromatin modifications are covalent
modifications that can effect transcription.
Adenosine-diphosphate ribosylation
Histone Acetylation
Associated with transcription activation.
Influence gene expression in (at least) two ways:
Neutralize Lysine’s positive charge, which can
weaken DNA-histone contacts, or histone-histone
Acetyl-Lysine is bound by a specific protein
domain that is found in many transcription
factors and calls bromodomain.
Rapidly reversible, and can turn over rapidly in
Histone Methylation
Characterized mainly for histone 3-lysin 4 (H3K4).
The Lysine can be mono-, di- or tri-methylated.
Doesn’t change the Lysine charge (naturally
methyl-Lysine can be bound by a methyl-lysin
binding domain, such as chromodomain, WD40
domain, Tudor domain, etc.
Research Challenges
Absence of sufficient verified data.
Contradictory evidences.
The available data is in a low resolution.
TAF1 as an acetyltransferase (HAT).
TAF1 and Gcn5 – is there a redundancy?
TAF1 and other HATs in yeast (Durant and Pugh).
Acetylation and methylation across promoters and
ORFs (Pokholok et al.)
High resolution mapping of acetylation and
methylation (Liu et al.)
Identifying two major groups with similar modification
patterns within.
Summary (Millar and Grunstein)
Genome-Wide Relationships
between TAF1 and Histone
Acetyltransferases in
Saccharomyces cerevisiae
Melissa Durant and B. Franklin Pugh
Molecular and Cellular Biology,
April 2006
The transcription machinery assembles at
promoters via two complexes, TFIID and
SAGA, which have a compensatory function
(Inna’s lecture…).
Both complexes contain subunits (TAF1 and
Gcn5) that harbor bromodomain and
acetyltransferase (HAT) activity.
In Saccharomyces cerevisiae, the bromodomains
appear on the TFIID-interacting protein Bdf1.
Do TAF1 and Gcn5 play redundant
role in yeast?
Gcn5, and not TAF1,
is important for bulk
H3 acetylation levels.
Promoter vs. Non-promoters regions
• TAF1 is not a major H3K9, H3K14 acetyltransferase (HAT).
• Gcn5 is a HAT at most yeast promoters.
Acetylation and Transcription
A strong correlation
between H3 K9, K14 in
W.T and without
transcription (without
A little REAL biology…
Acetylation of H4K8 is
dependant on Elp3, a HAT that
is associated with PolII during
elongation, while acetylation in
other sites in H4 might be less
PolII dependent.
Decrease in
and WT.
Gcn5 and TAF1 contribution to Gene
Recent studies: changes in gene expression for about
25% were observed only when both Gcn5 and TAF1
are eliminated.
If Gcn5 and TAF1 each make independent
contributions to transcription, the loss of both should
be equivalent to the multiplicative result (additive on a
log scale) of losing each individually.
If the two are functionally redundant, the double
mutant should result in an effect that is substantially
greater than the multiplicative effects of the individual
Gcn5 and TAF1 contribution to Gene
TAF1 and Gcn5
make independent
contribution to
gene expression No redundancy
in TAF1 and
Gcn5 function.
TAF1 redundancy with other HATs
Their is no (or a very little)
redundancy between TAF1 and
of the 5 tested HATs.
Some Other HATs and Acetylation
Why there is no effect of any HAT
mutant on acetylation?
(i) Having highly selective gene
(ii) Having Lysine specificities other
than those tested.
(iii) Making transient contributions.
(iv) Being highly redundant with other
TAF1 and Esa1
Esa1 is the main
HAT for H4
acetylation of K5,
K8, K12.
Taf1 and Gcn5 have no redundancy. In fact,
Taf1 may not be a HAT in yeast.
Transcription depends upon acetylation, but
acetylation doesn’t depend upon transcription.
Gcn5 and Esa1 have a major gene regulatory
HATs, but not Hat1, Elp3, Hpa2 and Sas3.
Genome-wide Map of Nucleosome
Acetylation and Methylation in Yeast
Dmitry K. Pokholok, Christopher T. Harbison, Stuart Levine,
Megan Cole, Nancy M. Hannett, Tong Ihn Lee, George W. Bell,
Kimberly Walker, P. Alex Rolfe, Elizabeth Herbolsheimer, Julia
Zeitlinger, Fran Lewitter, David K. Gifford, and Richard A.
Cell, August 2005
Global Nucleosome Occupancy
Nucleosome occupancy
at the promoter of
CPA1, a gene encoding
an amino acidbiosynthetic enzyme.
A composite profile of
histone occupancy at
5,324 genes.
Differential enrichment
of intergenic and genic
regions also occurred in
experiments lacking antibody.
After normalization to the
No substantial differences in the
relative levels of intergenic vs. genic
DNA at the average gene, but 40% of
the promoters have lower level of
histones than their transcribed genes.
Is there a correlation between gene
expression and nucleosome occupancy?
The genes were divided into five classes of
transcription level.
Before Normalization
After Normalization
Nucleosome occupancy is reduced
maximally at the promoters of active
Histone Acetylation
Two HATs were checked: Gcn5, which
acetylates H3K9 and H3K14, and Esa1, which
acetylates the four residues of H4.
The acetylation level were measured relative to
the histones level.
Histone Acetylation – results:
Histone Acetylation – Conclusion:
There is a positive association between Gcn5,
the modifications known to be catalyzed by
Gcn5, and transcriptional activity.
There is also a positive association between
Esa1, the modifications known to be catalyzed
by Esa1, and transcriptional activity, although
the association is not as strong as that observed
for Gcn5.
Three interesting trimethylation
patterns were observed
(Will be discusses later to details…)
Histone Methylation - conclusions
There is a positive correlation between H3K4
trimethylation near the 5’ end of transcribed
gene and transcription rate.
There is also a positive correlation between
H3K36 trimethylation near the 3’ end of
transcribed gene, and transcription rate.
Somewhat correlation exists between H3K79
trimethylation and transcription rate.
Single-Nucleosome Mapping of
Histone Modifications
in S. cerevisiae
Chih Long Liu, Tommy Kaplan, Minkyu Kim, Stephen
Buratowski, Stuart L. Schreiber, Nir Friedman, Oliver J. Rando
PLoS Biology, October 2005
For the first time, high-resolution measurement
of histone modifications.
Acetylation of H4K16
Transcription start
Methylation of H3K4:
Gradient from trimethylion in 5’, to dimethylation, and then
to mono-metylation
on the 3’.
Correlation between modification
the matrix of correlations between the 12
modifications shows that there are two groups
of strongly correlated acetylations:
Tri-methylation of
H3K4 correlates
with the larger
Mono- and dimethylation
orrelates with the
smaller group.
Principal Component Analysis PCA
81% of the variance in
histone modification
patterns is captured by
these two principal
Nucleosomes have
continuous variation, both in
the total level of acetylation,
and in the relative ratio of
the two groups of
modifications, but they do
not show much complexity
beyond these two axes.
Principal Component Analysis PCA
Component #1: Overall level of histone
Component #2: Relative levels of two groups
of histone modification - the “Transcription dependent modifications” that occur in 5’ to 3’
gradients over coding regions, and the
“Transcription - independent modifications”
that characterized by short hypo-acetyl domains
surrounding TSS.
Association Between Chromosomal
Location and Histone Modification
Coding region
In the PCA plot, it is easy to distinguish
between the promoters nucleosomes and the
genic nucleosomes.
5’ end
3’ end
Moreover, it is possible to distinguish
between the promoters nucleosomes and
different coding regions (5’, middle and 3’).
Specific genomic regions are characterized by
distinct modification patterns, with little overlap in
modification types between the different regions.
This correlation is imperfect, and it might be due to
the different expression level of the genes.
Is there a better correlation while separate genes
according to the PolII activity level?
5’ coding region
High PolII
activity level
PolII activity
Low PolII
activity level
Is there a difference between TSS
proximal nucleosomes and TSS
distal nucleosomes?
TSS proximal Correct
nucleosomes classification:
Modifications occur proximal
to transcribed gene contain
data about transcription level.
TSS distal Correct
nucleosomes classification:
Modifications occur distal to
transcribed gene can’t help
predict transcription level.
Association Between Modifications
and Transcription Factor Domains
Modification Boundaries
Tri-methylation for
nucleosome N-1
for nucleosome N
Example of “punctate” nucleosome
For the first time, modifications mapping in a
single-nucleosome resolution.
Two distinct groups of acetylation
The modification patterns can be explained by
only two principle components.
There is no “Histone Code”.
Genome-wide patterns of
histone modifications
in yeast
Catherine B. Millar and Michael Grunstein
Nature, September 2006
Histone Modification Enzymes
Substrate preference:
 In yeast, all known HMT methylate only one substrate.
 HATs and HDACs act on several sites, but have
distinct preferences.
Enzyme targeting:
 Specific targeting – recruitment by a transcription
factor/repressor. This can result in a class-specific
 Global – function over large regions, irrespective of
promoters and coding regions, and without TFs. Global
targeting thought to be independent on transcription
Histone Modification Enzymes –
Some HATs function as subunits in a few
complexes, one of them has a speciofic targeting
and the other has a global targeting.
Some HATs have a large but limited region –
usually enzymes that are involved in
heterochromation formation.
No specific HMTs are known to interact with
TFs, but some do recruit specifically to coding
Histone Modification Enzymes
Gradient of histone modifications in
Active Genes
Patterns of multiple histone
K-means clustering – identified groups of at
least 20 promoters that have a similar acetylation
state at 11 different sites, 53 clusters were
defined (kurdistany et al.).
The promoters within 55% of these clusters
share DNA-sequence motifs, whereas 26% bind
similar transcription factors, and 23% of clusters
contain promoters that lie upstream of genes
that belong to the same functional category.
Histone modifications in two
different clusters
Thanks for your listening,
!!!‫חנוכה שמח‬