Regulomics II:
Epigenetics and the histone code
Jim Noonan
GENE760
Biochemical indicators of regulatory function
1. TF binding
2. Histone
modification
3. Chromatin
modifiers &
coactivators
4. DNA looping
factors
• H3K27ac
p300
• H3K4me3
MLL
cohesin
Chromatin structure
nucleosome
H2A
H3
H2B
H4
H3 tail
Luger, Richmond & colleagues 1997
Chromatin structure
Zhou et al. Nat Rev Genet
12:7 (2011)
Covalent modifications on histones
me = methylation
ac = acetylation
ph = phosphorylation
ub = ubiquitination
H3
K27
ac
Histone
Residue
Modification
From Bannister and Kouzarides (2011) Cell Res 21:381
Covalent modifications on histones
me = methylation
ac = acetylation
ph = phosphorylation
ub = ubiquitination
H3
K27
me3
Histone
Residue
Modification
From Bannister and Kouzarides (2011) Cell Res 21:381
Histone modifications correspond to
functions in the genome
Zhou et al. Nat Rev Genet 12:7 (2011)
Histone modifications correspond to
functions in the genome
Zhou et al. Nat Rev Genet 12:7 (2011)
Histone modifications and chromatin accessibility
H3K4me3
H3K4me3
+ H3K27ac
At promoters of developmental regulator genes in ES cells
H3K27me3
Zhou et al. Nat Rev Genet 12:7 (2011)
Writers, readers and erasers of histone modifications
Tollervey and Lunyak (2012) Epigenetics 7:823
Ram et al., Cell 147:1628 (2011)
Writers, readers and erasers of histone modifications
MLL
p300
PRC2
KDM6B
From Bannister and Kouzarides (2011) Cell Res 21:381
Chromatin readers mediate functional outputs
Musselman et al. (2012) Nat Struct Mol Biol 19:1218
Chi et al. (2010) Nat Rev Cancer 10:457
There are many chromatin regulators
Ram et al., Cell 147:1628 (2011)
Histone variants
• Low abundance—limited copy number
• Primary sequence variation
• Specific functions
– CENP-A: centromere
– H3.3: transcription
– H2A.Z: euchromatin/
heterochromatin boundary, TSS
– H2A.X: genome integrity and high
order structure
From Tollervey and Lunyak (2012) Epigenetics 7:823
Genome browser interlude
Using chromatin profiling to
characterize biological systems
Comparing chromatin states across cell or tissue types
• Combinatorial analyses of histone modifications
• Global transcriptome profiling
• TF binding/motif analyses
Identify cell- and tissue-specific patterns
• Correlations among chromatin state, gene expression and function
Construct cell- and tissue-specific cis-regulatory maps
• Mapping chromatin regulators and TFs that control regulatory
elements
• Integrating tissue-specific expression with chromatin state and TF
data
Histone modification signal profiles
Transcription
factors
Pol II
Histone
mods
From Park (2009) Nat Rev Genet 10:669
Quantitative analysis of ChIP-seq signal profiles
HeLa K562
Histone
modification
signal
Signal at 20,000 bound sites
HeLa
Sites strongly
marked in HeLa
Sites
strongly marked
in both
Clustering
Sites
strongly
marked
in K562
Identifying chromatin state differences among
cell types
K-means clustering of histone modification signals at promoters across cell types
• Given a predetermined number of clusters (k), each
promoter is assigned to cluster with the nearest mean
Heintzman et al. Nature 459:108 (2009)
• Chromatin signatures at promoters tend to be more common across tissues
• Enhancers tend to be more tissue-specific
Identifying chromatin state differences among
cell types
Enhancers
Heintzman et al. Nature 459:108 (2009)
Cell-type specific enhancer activation correlates with
cell-type specific gene expression
Heintzman et al. Nature 459:108 (2009)
Integrated analysis of histone modifications identifies
functional ‘states’
Promoter
Chromatin mark observation frequency
Enhancer
ChromHMM: infer chromatin states from combinations of histone marks
• ‘emission’ probabilities associated with each chromatin state
• ‘transition’ probabilities – frequency in which chromatin states occur in
spatial relationships with each other along genome
Ernst et al., Nature 473:43 (2011)
Mapping and analysis of chromatin state dynamics
in nine human cell types
Cell types:
Marks:
•
H1 ESC
•
H3K4me3 (promoter/enhancer)
•
K562 (erythrocyte derived)
•
H3K4me2 (promoter/enhancer)
•
GM12878 (B-lymphoblastoid)
•
H3K4me1 (enhancer)
•
HepG2 (hepatocellular carcinoma)
•
H3K9ac (promoter/enhancer)
•
HUVEC (umbilical vein endothelium)
•
H3K27ac (promoter/enhancer)
•
HSMM (skeletal muscle myoblasts)
•
H3K36me3 (transcribed regions)
•
NHLF (lung fibroblast)
•
H4K20me1 (transcribed regions)
•
NHEK (epidermal keratinocytes)
•
H3K27me3 (Polycomb repression)
•
HMEC (mammary epithelium)
•
CTCF
Ernst et al., Nature 473:43 (2011)
Mapping and analysis of chromatin state dynamics
in nine human cell types
Ernst et al., Nature 473:43 (2011)
Chromatin states vary across cell types
Chromatin states at WLS:
Ernst et al., Nature 473:43 (2011)
Genetic drivers of gene regulatory variation
Furey and Sethupathy, Science
Disease-associated SNPs disrupt putative cell-type specific
enhancers
Ernst et al., Nature 473:43 (2011)
Chromatin state segmentation maps of the
human genome
Summary
• Histone modifications reveal where functions are encoded in the
genome
• Combinatorial analysis of histone modifications across biological states
identifies tissue-specific chromatin states
• Tissue-specific chromatin states reveal tissue-specific enhancers,
promoters, etc.
• Integrated analyses of chromatin states provide functional annotations
for predicting the effects of genetic variation