1. Regulomics II: Epigenetics and the histone code Jim Noonan GENE760

2. 1. TF binding Biochemical indicators of regulatory function 2. Histone modification H3K27ac H3K4me3 3. Chromatin modifiers & coactivators p300MLL 4. DNA looping factors cohesin

3. nucleosome H3 H4 H2A H2B Luger, Richmond & colleagues 1997 H3 tail Chromatin structure

4. Zhou et al. Nat Rev Genet 12:7 (2011)

5. H3 K27 ac HistoneResidueModification Covalent modifications on histones From Bannister and Kouzarides (2011) Cell Res 21:381 me = methylation ac = acetylation ph = phosphorylation ub = ubiquitination

6. H3 K27 me3 HistoneResidueModification From Bannister and Kouzarides (2011) Cell Res 21:381 Covalent modifications on histones me = methylation ac = acetylation ph = phosphorylation ub = ubiquitination

7. Zhou et al. Nat Rev Genet 12:7 (2011) Histone modifications correspond to functions in the genome

8. Zhou et al. Nat Rev Genet 12:7 (2011) Histone modifications correspond to functions in the genome

9. Histone modifications and chromatin accessibility H3K27me3 Zhou et al. Nat Rev Genet 12:7 (2011) H3K4me3 + H3K27ac At promoters of developmental regulator genes in ES cells

10. Tollervey and Lunyak (2012) Epigenetics 7:823 Ram et al., Cell 147:1628 (2011) Writers, readers and erasers of histone modifications

11. From Bannister and Kouzarides (2011) Cell Res 21:381 p300MLL PRC2 KDM6B Writers, readers and erasers of histone modifications

12. Musselman et al. (2012) Nat Struct Mol Biol 19:1218 Chi et al. (2010) Nat Rev Cancer 10:457 Chromatin readers mediate functional outputs

13. There are many chromatin regulators Ram et al., Cell 147:1628 (2011)

14. From Tollervey and Lunyak (2012) Epigenetics 7:823 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 Histone variants

15. Genome browser interlude

16. 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

17. Histone modification signal profiles Transcription factors Pol II Histone mods From Park (2009) Nat Rev Genet 10:669

18. Quantitative analysis of ChIP-seq signal profiles Histone modification signal Signal at 20,000 bound sites HeLa K562 Sites strongly marked in HeLa Sites strongly marked in K562 Clustering Sites strongly marked in both

19. Heintzman et al. Nature 459:108 (2009) 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 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

20. Heintzman et al. Nature 459:108 (2009) Identifying chromatin state differences among cell types Enhancers

21. Heintzman et al. Nature 459:108 (2009) Cell-type specific enhancer activation correlates with cell-type specific gene expression

22. Integrated analysis of histone modifications identifies functional ‘states’ 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) Promoter Enhancer Chromatin mark observation frequency

23. Mapping and analysis of chromatin state dynamics in nine human cell types Ernst et al., Nature 473:43 (2011) Cell types: H1 ESC K562 (erythrocyte derived) GM12878 (B-lymphoblastoid) HepG2 (hepatocellular carcinoma) HUVEC (umbilical vein endothelium) HSMM (skeletal muscle myoblasts) NHLF (lung fibroblast) NHEK (epidermal keratinocytes) HMEC (mammary epithelium) Marks: H3K4me3 (promoter/enhancer) H3K4me2 (promoter/enhancer) H3K4me1 (enhancer) H3K9ac (promoter/enhancer) H3K27ac (promoter/enhancer) H3K36me3 (transcribed regions) H4K20me1 (transcribed regions) H3K27me3 (Polycomb repression) CTCF

24. Mapping and analysis of chromatin state dynamics in nine human cell types Ernst et al., Nature 473:43 (2011)

25. Chromatin states vary across cell types Ernst et al., Nature 473:43 (2011) Chromatin states at WLS:

26. Furey and Sethupathy, Science 2013 Genetic drivers of gene regulatory variation

27. Ernst et al., Nature 473:43 (2011) Disease-associated SNPs disrupt putative cell-type specific enhancers

28. Chromatin state segmentation maps of the human genome

29. 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