Bio 483
October 9, 2012
Overview of
Histone Variants
Shelley
Berger
Shelley Berger
Biology;
CDB;
Genetics
The Wistar Institute
Penn Epigenetics Program
University of Pennsylvania
bergers@upenn.edu
Lecture Outline
What are histone variants?
Review nuclesome structure wrt replacement
Discuss H2A: macroH2A, H2A.Bbd,
H2Ax, H2AZ
H3: CENPA, H3.3
testes histone variants
Consideration of following issues:
- sequence variation
- nucleosome structure
- genome function
- location within the genome
- physiological function
Core vs. variant histones
N
globular
C
H3
H4
H2A
H2B
Are there additional histones?
H3
H4
H2A
H2B
H1
H3
H4
H2A
H3 ‘tail’
H2B
Luger and Richmond, Nature 1997
New nucleosome formation:
after replication
H3/H4 tetramer binds to DNA
2 dimers H2A/H2B bind H3/H4 tetramer
How to replace?
1. During replication assemble with variant
histones
2. H2A/H2B dimer exchange
3. Disassembly of nucleosome during
DNA damage repair, transcription
H2A
DNA repair
Gene
activation
Gene repression
X chrom inact
H2B
Gene
activation
H3
H4
Centromere
identity
H2A
Chromatin
compaction by
macroH2A
Chromatin
destabilization by
H2A.Bbd
H2A
H2Ax
Histone H2Ax
in DNA damage pathway
DNA damage leads to
complex repair pathways
Molecular details of DNA repair
H2Ax evolutionary conservation
H2Ax
phosphorylation
is an early step
in the repair
process
Histone H2AZ
in gene regulation
Histone H2AZ (= HTZ1):
What is its localization in the genome?
What genomic process does it regulate?
How does it affect NCP structure and positioning?
Genome-wide view of H2AZ at promotors
TSS
Promoter
TSS
Gene ORF
H2AZ tends to
occur in one nuc
up- and one nuc
down-stream of
the TSS
Does it
regulate
transcription?
Nuc “Depleted” Region
H2AZ is released as genes are activated
Its release is required for full activation
Is there a difference in nucleosome stability?
Association of H2A/H2AZ with chromatin
H2AZ is more loosely bound to chromatin
(although NCP structure very similar)
What is the localization of H2AZ
around active/inactive genes?
Active genes less enriched than inactive
H2AZ
What is its localization in the genome?
Inactive promoters
What genomic process does it regulate?
Poises genes for activation
How does it affect NCP structure and positioning?
Destablizes NCP:
correlates with depletion of one NCP over the TSS
How is it incorporated?
…a digression
ATP-dependent
Nucleosome Remodeling
Nucleosomes can be changed
in detailed association with DNA,
position, presence
Activities of ATP-dependent
chromatin remodeling enzymes
ATP
ADP + Pi
ATP
Remodeler
Evolutionary Tree of
SWI2/SNF2 Remodelers
ino80-sc
ISW1-Sc
ISW2-Sc
SNF2L-Hs
SNF2H-Hs
ISWI-Dm
CHD5-Hs
CHD4-Hs
CHD3-Hs
MI2-Dm
CHD1-Sc
CHD2-Hs
CHD1-Hs
CHD-Dm
STH1-Sc
SWI2-I
Brahma-Dm
BRG-1-Hs
BRM-Hs
INO80
ISWI
CHD
SWI/SNF
ATP dependent remodelers
and Histone Variant deposition
Swr1
H2AZ
Start with H2A NCPs
What do ATP-dependent
remodeling complexes do?
1. Directly alter NCP position
2. Exchange histones and histone variants:
New paradigm!
Model for H2AZ
Biochem. Cell Biol vol 84 2006
Instability of H2AZ NCPs allows high
temp to turn on/off genes in plants
Histone H3 and its Variants
Replication
Coupled
deposition
(only S phase)
CenpA
Replication
independent
Deposition
(not strictly
during S phase)
Histone H3.1 and H3.3
H3/H3.1
H3.3
H4
H3.3 is very similar to H3.1
H3.3 is
more
ancient
What genomic processes do
H3.1/H3.3 regulate?
Replication
Dependent:
Either
H3.1 or H3.3
Replication
Independent:
Only H3.3
H3.3 localizes with RNAPII and K4me
H3.3
H3.1
K4me2
RNAP
genes
How are H3.1 and H3.3 deposited
in RC and RI pathways?
H3.1 H3.3
p150
p60
HIRA
IP-Western
Two different chaperone/
assembly factors
Nucleosome assembly RC or RI
Histone CENPA
H3
CENPA
H4
What are centromeres?
Sequence complexity
CENPA, an
H3 variant,
is in a
specialized
NCP at
centromeres
in all
eukaryotes
Targeting of CENPA to centromeres
Mapping in vitro and
in vivo defined a
region in the histone
fold as “CATD”
Chaperone for Centromeric Localization
Cell line expressing
CENPA-TAP
HJURP required for
CENPA targeting to
centromeres
HJURP Knock Down
cell line
1. OE CENPA did not
restore targeting
2. H3-CATD recruited
by HJURP
No targeting
of CENPA in
HJURP KD
Controversy regarding structure of
the centromeric CENPA NCP
Proposed structures:
Is there a distinct structure?
(CENPA-H4)2 is more compact
Structure of CENPA NCP
Structural features map to CATD!
It forms a well
behaved octamer
Summary:
H3 variants and
their functions
Cenp
A
HIRA
CAF1
HJURP
Spermatogenesis and chromatin
compaction: key role for histone variants
Testes-specific histone variants
replace core histones following meiosis
All histones (except H4) have testes
variants
A remarkable variety of histone
variants to regulate the genome via
location-specific nuclesome funtion
H3
H4
H2A
H2B
H1
Penn
Epigenetics
Monthly
Meeting
Every month
Thursday
4:00 pm
Check website
Website:
Penn Epigenetics