Epigenetics

1
Epigenetics

• Xiaole Shirley Liu
• STAT115, STAT215, BIO298, BIST520

2
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?
• NIH epigenetics roadmap

3
Components

• DNA-methylation
• Nucleosome positioning
• Histone modifications
• DNase hypersensitivity
• Higher order chromatin struct
• Analogy

4
DNA CMG Methylation

• Close chromatin and repress gene expression,
  longer term effect
• Detecting DNA methylation in the genome
• mDIP-chip / seq antibody against CMG
• Methyl-seq m-specific
• restriction enzyme

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DNA Methylation

• Genome wide bisulfite sequencing
• Unmethyl C ? T
• High resolution, quantitative, but expensive!

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DNA Methylation

• 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
• In embryonic stem cells, there are also CHG
  methylation
• Recently, another type of DNA methylation called
  hydroxyl methylation (hmC) is found

7
Nucleosome Positioning

• Nucleosomal histones H2A, H2B, H3, H4
• Digest chromatin with MNase
• Hybridize to high (10bp step) resolution custom
  NimbleGen (50-mer probe) tiling microarrays

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Nucleosome Positioning on Arrays or Seq
Ozsolak et al Nat Biotech 2007
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Nucleosome Code

• Segal et al, Nat 2006
• MNase digested nucleosomes, sequenced 199
  nucleosomes
• See 10bp AA/TT/TA periodicity
• Kaplan et al, Nat 2009
• Sequenced over 20M yeast nuclesoomes
• Consider nucleosome avoidance of AT rich
  sequences in model

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Intrinsic seq explains more nucleosome depletion
(esp TSS and TTS) than nucleosome position
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Nucleosome Occupancy Histone Modification
Influence Factor Binding
TF
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Histone Modifications

• Different modifications at different locations by
  different enzymes

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Histone Modifications

• Gene body mark H3K36me3, H3K79me3
• Active promoter (TSS) mark H3K4me3
• Active enhancer (TF binding) mark H3K4me1
• Both enhancers and promoters H3K4me2, H3/H4ac,
  H2AZ
• Repressive promoter mark H3K27me3
• Repressive mark for DNA methylation H3K9me3

14
Nucleosome Occupancy Histone Modification
Influence Factor Binding
TF
15
Combine Tags From All ChIP-Seq
16
Extend Tags 3 to 146 nt Check Tag Count Across
Genome
17
Take the middle 73 nt
18
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

19
Higher Order Chromatin Interactions
Chromatin confirmation capture
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Hi-C

• Regions far by genomic distance are less likely
  to interact

Lieberman-Aiden et al, Science 2009
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Hi-C

• Ramen Noodle arrangement is less likely to form
  knots

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Transcription and Epigenetic Regulation

• Stem cell differentiation
• Aging brain
• Cancer?