Transcript Histone Modifications Associated with Heterochromatin and

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 H3K9
methylation by Clr4
Methylated H3K9 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)
BRCA1 Modifies Pericentric Heterochromatin
BRCA1 promotes enrichment of
Ub-H2A in pericentric heterochromatin
Loss of BRCA1 triggers transcription of
satellite-DNA in pericentric heterochromatin
Satellite-DNA transcription is sufficient to
induce genome instability after loss of BRCA1
from Venkitaraman, Nature 477, 169 (2011)
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