Epigenetics
Xiaole Shirley Liu
STAT115, STAT215, BIO298, BIST520
Epigenetics
• Heritable changes in gene function that occur
without a change in the DNA sequence
– How come not all the motif sites are bound by the
factor?
– How come TF binding only regulate some of the
nearby genes?
Epigenetics
• The study of heritable (transgenerational)
changes in gene activity that are not caused by
changes in the DNA sequence
• The study of stable, long-term alterations in the
transcriptional potential of a cell that are not
necessarily heritable
• Functionally relevant changes to the genome that
do not involve a change in the nucleotide
sequence
In Human
• Nature vs nurture
• Zygotic twins: same DNA different epigenome
• North American Ice Storm of 1998
Agouti Mice and DNA Methylation
The Making of a Queen
Larvae
From Ting Wang, Wash U
Queen
Worker
Epigenetic Landscape
Conrad Hal Waddington
(1905–1975)
Developmental biologist
Paleontologist
Geneticist
Embryologist
Philosopher
Founder for systems biology
Components
• DNA-methylation
• Nucleosome
position and
histone
modifications
• Chromatin
accessibility
• Higher order
chromatin
interactions
• Analogy
DNA Methylation Distribution in
Mammalian Genomes
• In human somatic cells, 60%-80% of all CpGs
(~1% of total DNA bases) are methylated
– Most methylation is found in “repetitive”
elements
• “CpG islands”, GC-rich regions that possess a high
density of CpGs, remain methylation-free
– The promoter regions of ~70% of genes have
CpG islands
From Ting Wang, Wash U
Two classes of DNA methyltransferases
(DNMTs)
Jones and Liang, 2009
Nature Review Genetics
Inheritance of DNA Methylation
From Ting Wang, Wash U
DNA Methylation Detection
• Bisulfite sequencing
– Unmethyl C  T
– High resolution, quantitative, but expensive!
From Wei Li, Baylor
BS-seq Methylation Call
• Most regions are either mostly methylated or
mostly unmethylated (dichotomy)
• Methylation level within a short distance is
consistent
ACGGGCTTACTTGCTTTCCTACGGGCTTACTTGCTTTCCTACGGGCTTACTTGCTTTCCTACGGGCTTACTTGC
CGGGTTTATTTGCTTTTTTATGGGC
TGGGTTTATTTGCTTTTTTATGGGC
TGGGTTTATTTGCTTTCCTATGGGC
CGGGCTTATTTGCTTTCCTATGGGC
CGGGCTTATTTGCTTTCCTATGGGC
3/5
60% methylated
From Ting Wang, Wash U
0/5
0% methylated
DNA Methylation Controls
Gene Expression
• Methylation at CpG islands often repress nearby
gene expression
• Many highly expressed genes have CpG
methylation on their exons
Some genes could
be imprinted, so
maternal and
paternal copies
have different
DNA methylation
From Ting Wang, Wash U
DNA Methylation in Cancer
• Prevalent misregulation of DNA methylation in
cancer: global hypomethylation and CpG island
hypermethylation
• Methylation variable regions in cancer
DNA Demethylation
• Recently, another type of DNA methylation
called hydroxyl methylation (hmC) is found
• hmC is an intermediate step between mC and C.
• TET family of proteins are important for DNA
demethylation
• Mutation in TET is linked to many cancers
Components
• DNA-methylation
• Nucleosome
position and
histone
modifications
• Chromatin
accessibility
• Higher order
chromatin
interactions
• Analogy
Nucleosome Occupancy & Histone
Modification Influence Factor Binding
TF
Histone Modifications
• Different modifications at different locations by
different enzymes
Histone Modifications in Relation to Gene Transcription
Bisulfite-Seq
H3K27ac
H3K4me1
H3K4me3
H3K36me3
H3K27me3
H3K9me3
RefSeq genes
SRPK1
SLC26A8
MAPK14
From Ting Wang, Wash U
Histone Modifications
• Gene body mark: H3K36me3, H3K79me3
• Active promoter (TSS) mark: H3K4me3
• Active enhancer (TF binding) mark: H3K4me1,
H3K27ac
• Both enhancers and promoters: H3K4me2,
H3/H4ac, H2AZ
• Repressive promoter mark: H3K27me3
• Repressive mark for DNA methylation:
H3K9me3
lncRNA Identification
• H3K4me3 active promoters
• H3K36me3 transcription elongation
Guttman et al, Nat 2009
23
24
25
Nucleosome Occupancy & Histone
Modification Influence Factor Binding
MNase digest
Antibody for
TF
Combine Tags From All ChIP-Seq
Extend Tags 3’ to 146 nt
Check Tag Count Across Genome
Take the middle 73 nt
Use H3K4me2 / H3K27ac Nucleosome
Dynamics to Infer TF Binding Events
/ac
/ac
/ac
/ac
/ac
Condition 1
Condition 2
Nucleosome Stabilization-Destabilization (NSD) Score
He et al, Nat Genet, 2010; Meyer et al, Bioinfo 2011
30
Condition-Specific Binding,
Epigenetics and Gene Expression
C1
C1
C2
C2
• Condition-specific TF bindings are associated
with epigenetic signatures
• Can we use the epigenetic profile and TF motif
analysis to simultaneous guess the binding of
many TFs together?
Genes
TF1
TF2
TF3
Epigenetics
31
Predict Driving TFs and
Bindings for Gut Differentiation
32
Identify Major TF Modules Regulating
Gut Differentiation and Function
GATA6
Cdx2
Embryonic and organ
development genes
Cdx2
HNF4
Metabolic and
digestive genes
• Nucleosome dynamics now applied to hematopoiesis and
cancer cell reprogramming
33
Verzi et al, Dev Cell, 2010
Components
• DNA-methylation
• Nucleosome
position and
histone
modifications
• Chromatin
accessibility
• Higher order
chromatin
interactions
• Analogy
DNase Hypersensitive (HS) Mapping
• DNase randomly cuts genome (more often in
open chromatin region)
• Select short fragments (two nearby cuts) to
sequence
• Map to
active
promoters
and
enhancers
Ling et al, MCB 2010
DHS Peaks
Capture Most TF
Binding Sites
• Motif occurrence in the
DHS peaks suggest TF
binding
• Quantitative signal
strength also suggest
binding stability
Thurman et al, Nat 2012
TF Network from DNase Footprint
37
DnaseI Cleavage vs Footprint
• Footprint occupancy score: FOS = (C + 1)/L + (C + 1)/R
• Smaller FOS value better footprint, for
L C R
predicting base resolution TF binding
GAT ACA
CTA TGT
38
DnaseI Cleavage vs Footprint
• Footprint occupancy score: FOS = (C + 1)/L + (C + 1)/R
• Smaller FOS value better footprint, for
L C R
predicting base resolution TF binding
• Intrinsic DNase cutting bias could
have 300-fold difference, creating fake footprints
GAT ACA
CTA TGT
CAGATA
CAGATC
…
ACTTAC
ACTTGT
0.004
0.004
1.225
1.273
39
Using DNaseI “Footprint” to
Predict TF Binding
• Using base-pair resolution cleavage pattern
(“footprint”) hurts TF binding prediction when it
is similar to intrinsic DNaseI cutting bias
40
Using DNaseI “Footprint” to
Predict Novel TF Motifs
41
He et al, Nat Meth 2013
Epigenetics and Chromatin
Transcription and Epigenetic Regulation
• Stem cell differentiation
• Aging brain
• Cancer