Chromatin modelinggene expression regulation

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Chromatin modeling-gene expression regulation

• Yi Jia
• BBMB676
• Mar. 28, 2006

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Outline

• Introduction
• Activities and mechanisms of ATP-dependent
  remodeling complexes
• Complex interactions in chromatin
• Summary

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Introduction

• Post-translational modifications of histone tails
• acetylation, phosphorylation, methylation etc.
• ATP-dependent remodeling
• ATP-dependent chromatin remodeling complex

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Jennifer A. Armstrong lab website
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ATP-dependent chromatin remodeling complex
Chromatin organisation modifier
acetyl-lysinebinding domain
Binding histone tail
Narlikar GJ, et al. Cell, 2002, 108475-487
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Relationship between SWI/SNF-class chromatin
remodeling complexes from yeast, Drosophila and
mammals
Mohrmann L and Verrijzer CP. B.B.A., 2005, 168159
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Diverse functions of different complexes in one
family
Modified from Mohrmann L and Verrijzer CP.
B.B.A., 2005, 168159
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Nucleosome Disruption by Human SWI/SNF Is
Maintained in the Absence of Continued ATP
Hydrolysis
Imbalzano AN, et al. J.B.C., 1996, 27120726
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Various activities of ATP-dependent chromatin
remodeling complexes

• All families can change position of nucleosomes
  on DNA (sliding nucleosomes)
• All can also form regularly spaced nucleosomes in
  a nucleosomal array
• ISWI-containing complexes appear to act primarily
  by nucleosome sliding
• SWI/SNF can change conformation of nucleosomes
  to expose nucleosomal DNA on surface of histone
  octamer without sliding nucleosome.

SNF2, not ISWI
SNF2 subfamily
SNF2, not ISWI
Nucleosome Sliding
ISWI family
Disassembly of nucleosomes?
Narlikar GJ, et al. Cell, 2002, 108475-487
SNF2 subfamily
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Mechanisms for nucleosome mobilisation
Flaus A and Owen-Hughes T. Current Opinion in
Genetics Development, 2004, 14165-173
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Mohrmann L and Verrijzer CP. B.B.A., 2005, 168159
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Chromatin Remodeling -Nucleosome Sliding
Mechanism
1) Used Isw2- mutant yeast strain grown on
raffinose, where 3 nuclesomes in promoter
region appear to be
shifted, leading to partial deregulation of gene.
2) Constructed gal-inducible allele of ISW2 w/
FLAG tag integrated into normal ISWI locus. 3)
Analyzed POT1 locus, a previously identified
target of Isw2. 4) Performed ChIP assays w/
anti-FLAG Ab for association of POT1 locus with
Iswi-FLAG (i.e, Iswi complex). 5) Showed Iswi2
complex increased assoc. with POT1 locus during
course of gal induction of Iswi.
Fazzio TC, et al. Molecular Cell, 2003,
121333-1340
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Fazzio TC, et al. Molecular Cell, 2003,
121333-1340
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Fazzio TC, et al. Molecular Cell, 2003,
121333-1340
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Chromatin remodeling by nucleosome disassembly
Nucleosome transaction catalyzed by RSC and ATP
in the presence of histone chaperones (Asf1,
Nap1)
Reversal of histone depletion by RSC and Asf1
and of nucleosome disassembly by RSC and Nap1.
Lorch Y, et al. PNAS, 2006, 1033090-3093
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Chromatin remodeling by nucleosome disassembly
Time course of nucleosome disassembly by RSC and
Nap1
RSC transfers histone octamers to Nap1 but not
to DNA or RNA
Lorch Y, et al. PNAS, 2006, 1033090-3093
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How are remodeling complexes targeted to
particular nucleosomes?

• 1) Non-targeting model SWI/SNF introduces
  transient changes in chromatin structure by a
  catalytic and random fashion throughout the
  genome, and that persistent, targeted changes in
  chromatin only occur in the presence of a
  DNA-binding transcription factor
• 2) Pol II association SWI/SNF may be targeted to
  specific genes by association with RNA pol II
  holoenzyme. But only a fraction of all pol II
  holoenzyme contains SWI/SNF.
• 3) Targeting by transcription factors SWI/SNF
  may be targeted to the correct genes by direct
  interaction and recruitment by gene-specific
  activators (and repressors).

Yudkovsky N, et al. Genes Development, 1999,
132369-2374
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Other Mechanisms for Targeting Remodeling
Complexes
Chromatin Remodeling Machine
a) Targeting by DNA-binding factors b)
Targeting by methylated DNA (for silencing) c)
Targeting by interaction w/ nuclear matrix
and actin-like proteins d) Targeting and
stabilization by modification pattern of
histones
Becker PB and Horz W, Annu Rev Biochem, 2002,
71247-273
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Recruitment of the SWI/SNF chromatin remodeling
complex by transcriptional activators
?Srb2 prevents pol II recruitment to
promoter rSrb recombinant Srb2 TBP1143N TBP
mutation rTBP recombinant TBP
SWI/SNF components
Immobilized templates used in assay
pol II components
1) Used template of His4 promoter w/ TATA box (
promoterless control) attached to magnetic
beads 2) Formed PICs w/ various yeast nuclear
extracts GAl4 washed away uncomplexed
proteins (using templates immobilized by magnetic
beads) 3) Detached promoter/PIC from beads by
PstI digestion 4) Western blotted PIC w/ Abs to
Swi3, Snf5, Rpb3, Gal11, TBP, Gal4

Yudkovsky N, et al, Genes Development, 1999,
132369-2374
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SWI/SNF is recruited to DNA by activators
independent of promoter sequences
G Gal4 DNA-binding domain only A Gal4-AH
(weak activation domain) V Gal4-VP16 (strong
activation domain) W His4 promoter template ?
promoterless template

STH1 component of RSC remodeling
complex
Yudkovsky N, et al, Genes Development, 1999,
132369-2374
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Repressor target ATP-dependent remodeling complex
Decreased expression of the SUC2 gene in isw2
mutants despite increased DNase I accessibility
of the upstream regulatory region
Increased DNase I accessibility and improperly
positioned nucleosomes at the POT1 locus in ISW2
mutant cells
Fazzio TG, et al, Molecular and cellular biology,
2001, 216450-6460
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Interactions between Complexes
IFN-ß promoter
HO promoter
Narlikar GJ, et al, Cell, 2002, 108475-487
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Proteins interacting with the SWI/SNF
chromatinremodelling complex

• Regulation of cell cycle
• Differentiation
• Transcription regulation
• Cancer
• Immunity

Iba H, Mizutani T and Ito T. Rev Med Virol, 2003,
1399-110
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Summary

• ATP-dependent chromatin remodeling complexes is
  conserved and diverse
• Remodeling actions can be classified into sliding
  and disassemble mechanisms
• Remodeling complexes can be targeted into
  specific chromatin by binding specific regulator
  and histone modification complex
• Many biologically important proteins can interact
  with chromatin complexes