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
Queen WorkerFrom Ting Wang, Wash U
Conrad Hal Waddington(1905–1975)Developmental biologistPaleontologistGeneticistEmbryologistPhilosopherFounder for systems biology
Epigenetic Landscape
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
ACGGGCTTACTTGCTTTCCTACGGGCTTACTTGCTTTCCTACGGGCTTACTTGCTTTCCTACGGGCTTACTTGCCGGGTTTATTTGCTTTTTTATGGGCTGGGTTTATTTGCTTTTTTATGGGCTGGGTTTATTTGCTTTCCTATGGGCCGGGCTTATTTGCTTTCCTATGGGCCGGGCTTATTTGCTTTCCTATGGGC
3/5 0/5
60% methylated 0% methylated
From Ting Wang, Wash U
DNA Methylation Controls Gene Expression
• Methylation at CpG islands often repress nearby gene expression
• Many highly expressed genes have CpG methylation on their exonsSome 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
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 200923
24
25
Nucleosome Occupancy & Histone Modification Influence Factor Binding
Antibody for
MNase digest
TF
Combine Tags From All ChIP-Seq
Extend Tags 3’ to 146 nt Check Tag Count Across Genome
Take the middle 73 nt
Nucleosome Stabilization-Destabilization (NSD) Score
Condition 1
Condition 2
Use H3K4me2 / H3K27ac Nucleosome Dynamics to Infer TF Binding Events
30
/ac /ac /ac
/ac /ac
He et al, Nat Genet, 2010; Meyer et al, Bioinfo 2011
Condition-Specific Binding, Epigenetics and Gene Expression
31Genes TF1 TF2 TF3 Epigenetics
• 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?
C1
C2
C1
C2
Predict Driving TFs and Bindings for Gut Differentiation
32
Identify Major TF Modules Regulating Gut Differentiation and Function
• Nucleosome dynamics now applied to hematopoiesis and cancer cell reprogramming
Verzi et al, Dev Cell, 2010
33
GATA6 Cdx2
Embryonic and organ development genes
HNF4
Metabolic and digestive genes
Cdx2
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
predicting base resolution TF binding
38
GAT ACA CTA TGT
L C R
DnaseI Cleavage vs Footprint
• Footprint occupancy score: FOS = (C + 1)/L + (C + 1)/R
• Smaller FOS value better footprint, for
predicting base resolution TF binding
• Intrinsic DNase cutting bias could
have 300-fold difference, creating fake footprints
39
GAT ACA CTA TGT
CAGATA 0.004CAGATC 0.004…ACTTAC 1.225ACTTGT 1.273
L C R
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
Components
• DNA-methylation• Nucleosome
position and histone modifications
• Chromatin accessibility
• Higher order chromatin interactions
• Analogy
HiC• In situ HiC has excellent resolution
• Domains conserved between cells and even species
43
HiC• Loops are
condition-specific– Assign binding
to genes
• Convergent CTCF at domain anchors– CTCF as
insulators
Epigenetics and Chromatin
45
Transcription and Epigenetic Regulation
• Stem cell differentiation• Aging brain• Cancer