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Heterochromatin
Darkly stained and condensed
Transcriptionally silent
and silences adjacent genes
Present at centromeres and telomeres
HP1 interacts with H3
only when K9 is methylated
Repressive structure can be propagated
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 6-33
Euchromatic gene placed in
heterochromatin is repressed
Histone Modifications Associated with Heterochromatin and Euchromatin
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 6-33
Initiation of Heterochromatin Assembly
from Grewal and Gia, Nature Rev.Genet. 8, 35 (2007)
Transcription factors and RNAi machinery bind to specific sequences
or repetitive elements to recruit histone modifying enzymes
Modified histones recruit HP1
HP1 recruits histone modifying enzymes to facilitate heterochromatin spread
Boundary elements prevent further heterochromatin spread
Mechanism of Heterochromatin Spreading
HP1 binds to H3K9me3
HP1 recruits SUV39H1 methylase
SUV39H1 methylates H3K9
on neighboring nucleosomes
from Bannister et al., Nature 410, 120 (2001)
Heterochromatin spreading is
restricted by boundary elements
Propagation of Heterochromatin
Passage of the replication fork releases
parental modified nucleosomes
Nucleosome binding sites are created
by recruitment of CAF1 by PCNA
CAF1-bound HP1 recruits
Suv39h, Dnmt1, and HDAC
Methylated histones provide
new HP1 binding sites
Structural RNA associates
from Maison and Almounzi, Nature Rev.Mol.Cell Biol. 5, 296 (2004)
Heterochromatin Functions
DNA or H3 methylation
recruits adaptors such as HP1
Adaptors recruit effectors that are
involved in chromosome segregation,
gene silencing, transcriptional
activation, and histone modification
from Grewal and Gia, Nature Rev.Genet. 8, 35 (2007)
Role of RNAi in Heterochromatin Formation in S. pombe
dsRNA is transcribed from centromeric
repeats or synthetic hairpin RNAs
dsRNA is processed to siRNA
siRNA promotes H3 K9
methylation by Clr4
Methylated H3 K9 recruits Swi6
to form silenced chromatin
Transcription of the top strand of
centromeric repeats is repressed
Rdp1 activity ensures
continuous dsRNA synthesis
from Schramke and Allshire, Science 301, 1069 (2003)
Recruitment of Clr4 by Swi6 chromatin
leads to spread of heterochromatin
Formation of Telomeric Heterochromatin
RAP1 binds to C1-3A repeats
Recruits Sir proteins
Overexpression of Sir3 causes
spread of telomeric heterochromatin
Silencing decreases
exponentially with distance
from Grunstein, Cell 93, 325 (1998)
Mechanism of Silencing at Telomeres
Sir2 deacetylates histones
Sir3,4 binds deacetylated histones
and recruits additional Sir2
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 7-35
Insulators Prevent the Progression of Condensed Chromatin
Insulators protect genes
from inappropriate signals
Insulators block the
action of distal enhancers
from West et al, Genes Dev. 16, 271 (2002)
Insulators prevent the
spreading of heterochromatin
gypsy Retrotransposon Contains an Insulator
gypsy protects a transgene from position effects
su(Hw) is necessary for enhancer blocking activity
gypsy contains a su(Hw) binding site
su(Hw) blocks the process that brings enhancer and promoter together
Formation of insulator bodies at the nuclear periphery
to divide the chromosome into looped domains
Multiple su(Hw) binding sites can inhibit enhancer blocking activity
Models for Heterochromatin Barrier Formation
Stable block interrupts
propagation of heterochromatin
Active barrier recruits a
complex containing
chromatin remodeling activity
from Donze and Kamakaka, BioEssays 24, 344 (2002)
Epigenetics
Heritable changes in gene function that cannot be explained by changes in gene sequences
DNA methylation
Histone variants and modifications
Nucleosome positioning
Epigenetic Modifications During Development
Epigenetically imposed restrictions to plasticity are erased in the germ line
Early mammalian development is characterized
by progressive restriction of cellular plasticity
accompanied by acquisition of epigenetic modifications
Epigenetic modifications impose a cellular memory
that accompanies and enables stable differentiation
Epigenetic Modifications Within an Arabidopsis Chromosome
Heterochromatin correlates with epigenetic marks
from Zhang, Science 320, 489 (2008)
DNA Methylation
Methylation at CpG residues
Sites of methylation
Inactive X
Imprinted loci
Transposon-derived sequences
CpG islands and CpG island shores
Methylation patterns are reproduced at each round of cell division
Methylated CpG Islands Inhibit Transcription
from Portela and Esteller, Nature Biotechnol. 28, 1057 (2010)
More than half of human promoters contain CpG islands
Promoters are usually unmethylated
Methylated DNA recruits methyl-CpG-binding domain proteins
which recruit histone modifying and chromatin-remodelling complexes
Unmethylated CpG islands recruit Cfp1 which associates
with a histone methyltransferase creating H3K4me3
Methylated CpG Islands Inhibit Transcription
from Portela and Esteller, Nature Biotechnol. 28, 1057 (2010)
More than half of human promoters contain CpG islands
Promoters are usually unmethylated
Methylated DNA recruits methyl-CpG-binding domain proteins
which recruit histone modifying and chromatin-remodelling complexes
Unmethylated CpG islands recruit Cfp1 which associates
with a histone methyltransferase creating H3K4me3
Methylation of Repetitive Sequences Stabilize Chromosomes
from Portela and Esteller, Nature Biotechnol. 28, 1057 (2010)
Unmethylated repetitive sequences cause reactivation of endoparasitic sequences
RNA-dependent DNA Methylation in Plants
Methylation occurs in transposons
and repetitive elements
PolIV transcribes ssRNA which is
converted to dsRNA by RDR2
siRNA is produced by DCL3
and loaded onto AGO4
from Law and Jacobsen, Nature Rev.Genet. 11, 204 (2010)
PolV produces IGN transcripts
and recruits AGO4
siRNA-IGN duplex is
formed and recruits DRM2
De Novo DNA Methylation in Mammals
DNMT3L interacts with
unmethylated H3K4
DNMT3A is recruited and activated
and forms a tetrameric complex
Active sites are separated
by 8-10 bp and methylates
opposite DNA strands
from Law and Jacobsen, Nature Rev.Genet. 11, 204 (2010)
Tetramer oligomerizes and results
in 10 bp pattern of methylation
on the same strand
Establishment of DNA Methylation Pattern
Most CpGs are unmethylated
before implantation
RNA pol II recruits
H3K4 methyltransferase
DNMT3L only binds unmethylated H3K4
and recruits DNA methyltransferases
from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009)
Propagation of DNA Methylation State
Newly synthesized methylated
DNA is hemimethylated
NP95 binds hemimethylated DNA
DNMT1 is a maintenance
methyltransferase and binds PCNA
NP95 links DNMT1
to hemimethylated DNA
from Richly et al., BioEssays 32, 669 (2010)
Mechanisms for Repression Mediated by MBD Proteins
from Wade, BioEssays 23, 1131 (2001)
MeCP2 Regulates Gene Expression in Response to Neural Activity
Rett Syndrome is linked to mutations
in MECP2 on the X chromosome
MeCP2 binds CpG residues and
silences target genes such as BDNF
and corticotropin-releasing hormone
from Bienvenu and Chelly, Nature Rev.Genet. 7, 415 (2006)
from Miller, Science 314, 1356 (2006)
Neural activity triggers
MeCP2 phosphorylation
and target gene activation
Hippocampal neurons grow
dendrites with fewer branches
when MeCP2 is blocked
Establishment of Cell Identity in Drosophila Embryos
Segment identity is established by sequential
spatially-localized expression of specific genes
Regulatory genes are expressed transiently
Transcriptional memory is
maintained throughout development
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-24
Misexpression of Homeotic Genes Lead to Morphological Abominations
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-25
Polycomb and Trithorax Complexes
Prevents changes in cell identity by preserving transcription patterns
Chromatin is altered in a heritable manner
Polycomb-group Proteins
Maintains a silenced state
Prevents chromatin remodelling
Trithorax-group Proteins
Maintains an active state
Counteracts the action of PcG proteins
Memory system composed of PcG and trxG complexes is linked to the histone code
Model for PcG Formation and Function
PcG complexes are recruited to PREs
PRC2 complex methylates
H3 K9 and K27
H3K27me3 recruits
Polycomb and PRC1 complex
H3K27me3 is segregated to both
daughter DNAs to maintain repression
from Lund and van Lohuizen, Curr.Opin.Cell Biol. 16, 239 (2004)
Propagation of H3K27 Methylation
EED2 binds H3K27me3
EED2 binding stimulates PRC2 activity
EZH2 methylates H3K27
from Richly et al., BioEssays 32, 669 (2010)
Demethylation of H3K27me3 Promotes Gene Activation
PRC2 is recruited to H3K27me3
to mediate gene repression
UTX and JMJD3 are recruited to
Hox promoters and reverse repression
Change in cell fate is mediated by
H3K27 demethylation and H3K4
methylation, whose activities are
present in the same complex
from Rivenbark and Strahl, Science 318, 403 (2007)
Trithorax Complex Mechanism of Action
TrxC methylates H3K4 and recruits HAT and remodeling complexes
Acetylated H3K9 prevents methylation, and prevents HP1 binding
Somatic Cell Reprogramming
Pleuripotency genes in somatic cells
have methylated CpG islands
Epigenetic marks must be
reset to generate induced
pleuripotent stem (iPS) cells
from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009) Repressive histone methylation
marks must be removed, followed
by removal of DNA methylation
which activates the gene
Epigenetics and Heart Failure
Brg1, a SWI/SNF component,
is activated by cardiac stress
Brg1 suppresses expression of a
CKI to promote myocyte proliferation
Brg1 promotes reprogramming to
an embryonic state of transcription
Brg1 forms a complex with
HDAC and PARP and triggers a shift
from a-myosin heavy chain expression
to b-myosin heavy chain expression
from Hang et al., Nature 466, 62 (2010)
Epigenetic Modifications May Drive Cognitive Decline
Chromatin remodeling in the
hippocampus is necessary for
stabilizing long term memories
Aged mice have lower H4K12 acetylation
HDAC inhibitor restores H4K12
acetylation and improved memory function
from Sweatt, Science 328, 701 (2010)
SIRT1 Deacetylase and Alzheimer’s Disease
SIRT1 deacetylates RARb
SIRT1 lof causes Alzheimer’s-like phenotype
SIRT1 lof results in decreased a-secretase
transcription and increased Ab production
from Wolfe and Selkoe, Cell 142, 194 (2010)
SIRT1 lof causes decreased
Notch pathway activity and
decreased neuronal repair
Prion Epigenetics
Prions template conformational conversion
of other molecules of the same protein
Prions are formed through an oligomeric
nucleus, and the elongating polymer is
severed by protein remodeling factors
Prions are disseminated to
daughter cells during cell division
from Halfmann and Lindquist, Science 330, 629 (2010)
Stress Accelerates Prion Appearance
Abrupt changes have consequences
for protein folding
Prion-free cells are adapted to
environment 1, but poorly
adapted to environment 2
Prion formation and disappearance
provide fitness advantages in
different environments
from Halfmann and Lindquist, Science 330, 629 (2010)
Prions connect environmental
conditions to acquisition and
inheritance of new traits
Co-suppression
Increase in gene copy number
results in decreased expression
Dependent on PcG genes
PcG complexes interact in trans
from Pirrotta, Cell 93, 333 (1998)
Imprinting
Expression of only one allele of a locus
Only 80 genes in mammals are imprinted
Most imprinted genes are involved in growth control
Imprinted genes involves allele specific methylation
and is resistant to genome-wide demethylation
Clusters of imprinted genes contain noncoding RNAs
that are involved control allele-specific expression
Imprinted Expression of the H19 and Igf2 Genes
Maternal – H19 expression
Paternal – Igf2 expression
from Reik and Murrell, Nature 405, 408 (2000)
Imprinting is Regulated by a Methylation-sensitive Boundary
ICR is methylated in the male germ line
ICR is protected from methylation
in the female germ line by CTCF
CTCF binding to the ICR in
females prevents activation of
Igf2 by downstream enhancer
from Reik and Murrell, Nature 405, 408 (2000)
In males, the downstream enhancer
activates Igf2 and H19 expression
is repressed by DNA methylation
Imprinting of the PWS-AS Locus
from Ferguson-Smith and Surani, Science 293, 1086 (2001)
The AS-ICR is required for methylation and inactivation
of the PWS-ICR in females to repress nearby genes
The AS-ICR is nonfunctional in males allowing
the PWS-ICR to activate nearby genes
The PWS-ICR promotes expression of an antisense Ube3a transcript in males
Dosage Compensation Mechanisms
Genomes compensate for different
numbers of sex chromosomes by
adjusting gene expression levels
from Straub and Becker, Nature Rev.Genet. 8, 47 (2007)
X Inactivation in Mammals
X inactivation is initiated from the Xic
Xist and Tsix partially overlap
and are transcribed in opposite
directions from the Xic
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 22-7
Model for the Initiation of X Inactivation
The Xic in female cells colocalize prior to X inactivation
Low expression of Tsix from Xi leads to Xist transcription
Xist RNA coats the Xi in cis
The chromatin structure of Xi becomes condensed
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 22-7
Stepwise Progression of X Inactivation in Differentiating ES Cells
One X chromosome is converted
to facultative heterochromatin
Xist transcription off the inactive X
initiates chromatin modification events
X inactivation is maintained epigenetically
from Brockdorff, Trends Genet. 18, 352 (2002)
Calico Cats
One of the genes controlling fur
color is on the X chromosome
B – orange
b - black
Female mammals are genetic mosaics
Random X inactivation early in embryonic development
leads to patchworks of skin cells expressing each allele
The Dosage Compensation Complex in Drosophila
SXL in females prevents MSL2 translation
MSL2 in males stabilizes
roX, MSL1, and MSL3
DCC binds to high affinity
sites on X chromosome
from Gilfillan et al., FEBS Lett. 567, 8 (2004)
DCC spreads to nearby
sites on active chromatin
H4K16 acetylation impedes formation
of condensed chromatin structure
DCC is Localized to the X Chromosome
DCC localization is determined
by staining of polytene
chromosomes with anti-MSL1
DCC associates almost exclusively
with transcribed regions
from Straub and Becker, Nature Rev.Genet. 8, 47 (2007)