1. 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
Euchromatic gene placed in
heterochromatin is repressed
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 6-33

2. Histone Modifications Associated with Heterochromatin and Euchromatin
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 6-33

3. 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

4. Mechanism of Heterochromatin Spreading
HP1 binds to H3K9me3
HP1 recruits SUV39H1 methylase
SUV39H1 methylates H3K9
on neighboring nucleosomes
Heterochromatin spreading is
restricted by boundary elements
from Bannister et al., Nature 410, 120 (2001)
H1 recruits Su(var)3-9 to heterochromatin
resulting in transposon silencing

5. Propagation of Heterochromatin
from Maison and Almounzi, Nature Rev.Mol.Cell Biol. 5, 296 (2004)
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

6. 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)

7. 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
Recruitment of Clr4 by Swi6 chromatin
leads to spread of heterochromatin
from Schramke and Allshire, Science 301, 1069 (2003)

8. 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

9. CTCF Regulates Genome Architecture
CTCF colocalizes with cohesin
CTCF mediates long-range
interactions between genomic sequences
CTCF establishes domains in which
genes are coregulated and targets
regulatory sequences to their promoters
from Ong and Corces, Nature Rev.Genet. 15, 234 (2014)

10. Assays for Barrier Insulator Activity
Barrier insulators protect transgene
from position-effect silencing
Functional borders may require
several different mechanisms
including CTCF binding
The function of insulators is to maintain
higher-order folding and establish
topologically associating domains
From Phillips-Cremins and Corces, Mol.Cell 50, 461 (2013)

11. Assay for Enhancer-blocking Insulators
block the action of distal enhancers
Most CTCF binding sites do not
act as enhancing-blocking insulators
Enhancer-blocking may be more
important in small genomes because of a
greater need to regulate enhancer specificity
From Phillips-Cremins and Corces, Mol.Cell 50, 461 (2013)

12. 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

13. 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)

14. 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)

15. Epigenetics
Heritable changes in gene function that cannot be explained by changes in gene sequences
DNA methylation
Histone variants and modifications
Nucleosome positioning

16. 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

17. Epigenetic Modifications Within an Arabidopsis Chromosome
Heterochromatin correlates with epigenetic marks
from Zhang, Science 320, 489 (2008)

18. DNA Methylation
Methylation at CpG residues correlates with gene repression
5meC is involved in stable epigenetic repression
Sites of methylation
Inactive X
Imprinted loci
Transposon-derived sequences
CpG islands are CpG-rich regions usually found at promoters
Methylation patterns are reproduced at each round of cell division

19. 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

20. Methylation of Repetitive Sequences Stabilize Chromosomes
from Portela and Esteller, Nature Biotechnol. 28, 1057 (2010)
Unmethylated repetitive sequences cause reactivation of endoparasitic sequences

21. RNA-dependent DNA Methylation in Plants
from Matzge and Mosher, Nature Rev.Genet. 15, 394 (2014)
Pol IV is recruited to chromatin and transcribes ssRNA which is converted to dsRNA by RDR2
siRNA is produced by DCL3 and loaded onto AGO4
Pol V transcribes a scaffold RNA that base pairs with AGP4-bound siRNA
DNA is unwound and DRM2 is recruited and methylates DNA
Histones are modified to reinforce the silenced state

22. 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

23. 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)

24. 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)

25. DNA is Demethylated by TET Proteins
5mC is oxidated iteratively by TET
5hmC is reverted to unmodified C by
passive dilution during DNA replication
Oxidative products are excised by thymine
DNA glycosylase and repaired by BER
from Kohli and Zhang, Nature 502, 472 (2013)

26. Rett Syndrome Onset of symptoms in humans is 6-12 months of age
Rett syndrome is a severe neurological disorder
Abnormal head growth
Decrease in speech function
Breathing disturbances
Repetitive hand movements
Caused by mutation in the MeCP2 gene on the X chromosome

27. MeCP2 Function and Rett Syndrome
from Lyst and Bird, Nature Rev.Genet. 16, 261 (2015)
MeCP2 binds methylated DNA, but also binds to unmethylated DNA via regions outside the MBD
MeCP2 compacts chromatin structure
MeCP2 recruits a corepressor complex that contains a histone deacetylase

28. MeCP2 Regulates Gene Expression in Response to Neural Activity
MeCP2 binds methylated DNA and
silences target genes such as BDNF
and corticotropin-releasing hormone
Neural activity triggers
MeCP2 phosphorylation
and target gene activation
from Bienvenu and Chelly, Nature Rev.Genet. 7, 415 (2006)
Hippocampal neurons grow
dendrites with fewer branches
when MeCP2 is blocked
Increase in mCH sequences after birth is
enriched in genes with neuronal functions
from Miller, Science 314, 1356 (2006)

29. Many MeCP2-Repressed Genes Encode
Proteins That Modulate Neuronal Physiology
MeCP2 binds mCA
Density of mCA is higher in long genes
Frequency of mCA increases with age
Long genes are selectively expressed in the brain
Length- and mCA-dependent increase in gene expression in MeCP2 mutants
from Gabel et al., Nature 522, 89 (2015)