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 positioningNucleosome positioning Histone modificationsHistone modifications DNase hypersensitivityDNase hypersensitivity Higher order chromatin structHigher order chromatin struct Analogy

4. DNA C M G Methylation Close chromatin and repress gene expression, longer term effect Detecting DNA methylation in the genome –mDIP-chip / seq: antibody against C M G –Methyl-seq: m-specific restriction enzyme

5. DNA Methylation Genome wide bisulfite sequencing –Unmethyl C  T –High resolution, quantitative, but expensive!

6. 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

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

9. 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

10. Intrinsic seq explains more nucleosome depletion (esp TSS and TTS) than nucleosome position

11. Nucleosome Occupancy & Histone Modification Influence Factor Binding TF

12. Histone Modifications Different modifications at different locations by different enzymes

13. 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 Antibody for MNase digest 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

20. Hi-C Regions far by genomic distance are less likely to interact Lieberman-Aiden et al, Science 2009

21. Hi-C Ramen Noodle arrangement is less likely to form knots

22. Transcription and Epigenetic Regulation Stem cell differentiation Aging brain Cancer?