Chromatin Structure II: histone code and chromatin structure during DNA replication and repair

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Chromatin Structure II histone code and
chromatin structure during DNA replication and
repair
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Different post-translational modifications of the
histone tails are observed during different
cellular processes
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Enzymes that post-translationally modify core
histone tails
Shilatifard, Ann Rev Biochem 75243, 2006
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Examples of combinatorial modifications in
histone NH2-terminal tails that likely represent
imprints for active or inactive chromatin
Jenuwein and Allis, Science 293 1074, 2001
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Synergistic or antagonistic modifications in
histone H3 and H4 amino termini
Jenuwein and Allis, Science 293 1074, 2001
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Translating the histone code Protein modules of
histone modifying enzymes interact with
site-specific modification marks in histone tails
Jenuwein and Allis, Science 293 1074, 2001
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Interactions between histone- and DNA-methylating
enzymes can be induced or stabilized by
site-selective combinations of methylation marks
Jenuwein and Allis, Science 293 1074, 2001
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Maintenance and spreading of heterochromatin
Shilatifard, Ann Rev Biochem 75243, 2006
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Replication- and Repair-Coupled Chromatin
Dynamics and Cell Identity
Groth et. al, Cell 128, 721, 2007
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Chromatin challenges at the replication fork

• DNA template has to be accessed
• Nucleosomal organization has to be reproduced on
  daughter strands

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• Mechanism?
• Ahead of moving fork, parental nucleosomes
  disrupted into H2A-H2B dimers and (H3-H4)2
  tetramers
• Tetramers transferred onto daughter strands in
  random fashionmay allow PTMs and histone
  variants to be maintained
• Segregation mechanism operates together with de
  novo nucleosome assembly to fully reproduce
  nucleosomal density on daughter strands
• Basic substrates for de novo deposition H3-H4
  dimers (diacetylated at H4 K5/K12)
• How are these 3 events coordinated to preserve
  genetic stability and reproduce epigenetic marks?

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Chromatin challenges at the replication fork
Groth et. al, Cell 128, 721, 2007
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PCNA bridge between genetic (DNA polymerase
processivity factor) and epigenetic (platform for
chromatin restoration) is retained on newly
synthesized DNA 20 min (about 40kb)could
represent time of chromatin maturation. recruits
multiple chromatin modulating factors, some of
which can recruit additional factors
Groth et. al, Cell 128, 721, 2007
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Model for maintenance of silent chromatin
replication-coupled nucleosome assembly
Newly assembled nucleosomes
HP1 proteins
H3K9Me

• Existing silent nucleosomes
• (black)
• disrupted by replication machinery and
  accompanying remodeling complexes
• histones randomly segregated to two daughter
  strands.

• What directs methylation of new nucleosomes? 2 of
  the possibilities
• HMTases bound to HP1 on adjacent nucleosomes
• Methylation and HP1 binding are coupled to
  nucleosome assembly

Vermaak, Ahmad, Henikoff, Curr.Opin.Cell Biol.
15266, 2003
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Model for chromatin disassembly and assembly
during DNA replication
Is this passive (displaced by advancing
replication machinery) or active (mediated by
specific chromatin disassembly factors)?

• Histone chaperones CAF-1 (chromatin assembly
  factor 1) Asf1 (anti-silencing function 1)
• ACF? ATP-dependent chromatin remodelers

Linger and Tyler, Mutation Res. 618, 52, 2007
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Question regarding mechanism of de novo
nucleosome assembly and epigenetic inheritance

• Are histone PTMs imposed prior to (on soluble
  histone dimers) or after their incorporation into
  chromatin (on nucleosomal histones)?
• Experimental evidence to support both
• May be differences depending on the particular
  histone modification and where/when the enzymes
  are present to add the specific modification

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Inactivation of particular histone chaperones and
ATP-dependent chromatin remodelers leaves cells
hypersensitive to DNA damaging agents further
studies demonstrated specific roles during DNA
repair
Linger and Tyler, Mutation Res. 618, 52, 2007
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Challenges for resetting epigenetic marks after
DNA repair
Coordination of DNA repair and chromatin dynamics
is required to ensure maintenance of both genetic
and epigenetic information after DNA damage

• Lesion has to be made accessible for repair
  enzymes
• Lesion has to be repaired
• Chromatin organization has to be restored after
  repair

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DNA damage checkpoint detects and signals the
presence of DNA damage and arrests cell cycle
progression until damage is repaired

• Initiated by recruitment of multiple checkpoint
  components to DSB by DNA repair machinery (eg.
  ATR kinase)
• ATR phosphorylate and activate downstream targets
  in damage checkpoint signaling cascade (eg.
  Histone H2AX is phosphorylated on S139 in
  chromatin flanking the lesion
• After DNA repair, H2AX must be dephosphorylated
  to recover from DNA damage checkpoint
• This dephosphorylation can only happen after
  disassembly of P-H2AX from chromatin

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Resetting the epigenetic landscape after DNA
repair
Groth et. al, Cell 128, 721, 2007
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• During repair process, chromatin surrounding the
  lesion is rearranged and modified to recruit
  checkpoint and repair factors
• (example H2AX phosphorylation)
• Restoration process
• Nucleosome reassembly through recycling or
  deposition of new histones
• Clearance of PTMs imposed during lesion detection
  and repair
• Restoration of specific domains
• Questions
• What is fidelity of restoration process?
• Do genotoxic insults challenge epigenetic
  stability?

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Only approx. 30bp excised and replaced
(theoretically chromatin remodeling or lateral
histone movement should be sufficient), but data
indicates that chromatin disassembly/reassembly
occur during NER, and are also required for
viability after NER
Chromatin assembly/ disassembly requires histone
chaperones, whereas chromatin remodeling does not
Linger and Tyler, Mutation Res. 618, 52, 2007
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Linger and Tyler, Mutation Res. 618, 52, 2007
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Linger and Tyler, Mutation Res. 618, 52, 2007