shelley berger the wistar institute university of pennsylvania
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Bio 483 October 9 , 2012. Overview of Histone Variants. Shelley Berger Biology; CDB; Genetics Penn Epigenetics Program [email protected]. Shelley Berger The Wistar Institute University of Pennsylvania. Lecture Outline. What are histone variants? - PowerPoint PPT PresentationTRANSCRIPT
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Shelley BergerThe Wistar InstituteUniversity of Pennsylvania
Overview of Histone Variants
Bio 483October 9, 2012
Shelley BergerBiology; CDB; GeneticsPenn Epigenetics [email protected]
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Lecture OutlineWhat are histone variants?Review nuclesome structure wrt replacement
Consideration of following issues: - sequence variation - nucleosome structure- genome function- location within the genome- physiological function
Discuss H2A: macroH2A, H2A.Bbd, H2Ax, H2AZH3: CENPA, H3.3
testes histone variants
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Core vs. variant histonesH3
H4
H2A
H2B
globularN C
Are there additional histones?
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H2A
H2B
H3
H4
H1
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Luger and Richmond, Nature 1997
H3
H4
H2A
H2B H3 ‘tail’
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New nucleosome formation: after replication
H3/H4 tetramer binds to DNA
2 dimers H2A/H2B bind H3/H4 tetramer
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How to replace?
1. During replication assemble with variant histones
2. H2A/H2B dimer exchange
3. Disassembly of nucleosome during DNA damage repair, transcription
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H2A
H2B
H3
H4
DNA repair
Gene repressionX chrom inact
Gene activation
Centromere identity
Gene activation
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H2A
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Chromatin compaction by
macroH2A
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Chromatin destabilization by
H2A.Bbd
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H2AxH2A
Histone H2Axin DNA damage pathway
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DNA damage leads to complex repair pathways
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Molecular details of DNA repair
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H2Ax evolutionary conservation
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H2Ax phosphorylation is an early step
in the repair process
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Histone H2AZ (= HTZ1):
How does it affect NCP structure and positioning?
What is its localization in the genome?What genomic process does it regulate?
Histone H2AZin gene regulation
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Genome-wide view of H2AZ at promotors
TSS
Nuc “Depleted” Region
Gene ORFPromoter
TSS
H2AZ tends to occur in one nuc up- and one nuc down-stream of the TSS
Does it regulate transcription?
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H2AZ is released as genes are activated Its release is required for full activation
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Association of H2A/H2AZ with chromatin
H2AZ is more loosely bound to chromatin (although NCP structure very similar)
Is there a difference in nucleosome stability?
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What is the localization of H2AZaround active/inactive genes?
Active genes less enriched than inactive
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H2AZ
How does it affect NCP structure and positioning?
What is its localization in the genome?
What genomic process does it regulate?
Inactive promoters
Poises genes for activation
Destablizes NCP:correlates with depletion of one NCP over the TSS
How is it incorporated?
…a digression
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Nucleosomes can be changedin detailed association with DNA,
position, presence
ATP-dependentNucleosome Remodeling
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Activities of ATP-dependent chromatin remodeling enzymes
ATP ADP + Pi
ATPRemodeler
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Evolutionary Tree of SWI2/SNF2 Remodelers
BRM-HsBRG-1-HsBrahma-DmSWI2-I
STH1-ScCHD-Dm
CHD1-HsCHD2-HsCHD1-ScMI2-DmCHD3-HsCHD4-Hs
CHD5-HsISWI-DmSNF2H-Hs
SNF2L-HsISW2-ScISW1-Sc
ino80-sc
SWI/SNF
ISWI
CHD
INO80
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Start with H2A NCPs
ATP dependent remodelersand Histone Variant deposition
Swr1
H2AZ
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What do ATP-dependent remodeling complexes do?
2. Exchange histones and histone variants:New paradigm!
1. Directly alter NCP position
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Biochem. Cell Biol vol 84 2006
Model for H2AZ
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Instability of H2AZ NCPs allows high temp to turn on/off genes in plants
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Histone H3 and its Variants
CenpA
ReplicationCoupleddeposition(only S phase)
Replicationindependent Deposition(not strictlyduring S phase)
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H3/H3.1
H4
H3.3
Histone H3.1 and H3.3
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H3.3 is very similar to H3.1
H3.3 is more ancient
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What genomic processes do H3.1/H3.3 regulate?
ReplicationDependent:EitherH3.1 or H3.3
ReplicationIndependent:Only H3.3
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H3.3 localizes with RNAPII and K4me
genes
RNAP
K4me2
H3.1
H3.3
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H3.1 H3.3
How are H3.1 and H3.3 deposited in RC and RI pathways?
HIRA
IP-WesternTwo different chaperone/
assembly factors
p150
p60
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Nucleosome assembly RC or RI
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CENPAH3
H4
Histone CENPA
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What are centromeres?
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Sequ
ence
com
plex
ity
CENPA, an H3 variant, is in a specialized NCP at centromeres in all eukaryotes
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Targeting of CENPA to centromeres
Mapping in vitro and in vivo defined a region in the histone fold as “CATD”
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Chaperone for Centromeric Localization
Cell line expressingCENPA-TAP
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HJURP required for CENPA targeting to centromeres
HJURP Knock Down cell line
No targeting of CENPA in HJURP KD
1. OE CENPA did not restore targeting2. H3-CATD recruited by HJURP
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Controversy regarding structure of the centromeric CENPA NCP
Proposed structures:
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Is there a distinct structure?
(CENPA-H4)2 is more compact
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Structure of CENPA NCP
Structural features map to CATD!
It forms a well behaved octamer
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CenpA
HJURPHIRACAF1
Summary: H3 variants and their functions
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Spermatogenesis and chromatin compaction: key role for histone variants
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Testes-specific histone variants replace core histones following meiosis
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All histones (except H4) have testes variants
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H2A
H2B
H3
H4
H1
A remarkable variety of histone variants to regulate the genome via location-specific nuclesome funtion
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