ENCODE Chromatin Groups

1. ENCODE Chromatin Groups Broad / MGH (Bernstein, Kellis) Duke / UNC / UT (Crawford, Lieb, Iyer) UW (Stamatoyannopoulos) Umass (Dekker)

2. ENCODE Chromatin Structure and Regulatory Elements • Dnase Hypersensitivity • Histone Modifications • Chromatin Proteins • FAIRE • 5C • Promoters • Transcripts • Enhancers • Silencers • Insulators • Long-range interactions • Chromatin Element Dynamics • Enhancer-Gene Linkages • Regulatory Motifs

3. Highlights • Robust pipelines enabling high coverage of cellular diversity • Analytical framework guiding epigenomic studies worldwide • Distinct functional elements & regulatory motifs (millions…) • Genotype-related variability • Distal elements connected directly with cognate promoters • Generality & cellular diversity >>> widespread use by community

4. Broad coverage of human cellular space:

5. A comprehensive catalogue will require deep cell space sampling Acknowledgements Marked cellular diversity, potentially millions of elements Unique DNaseI Hypersensitive Sites Mapped Cell Types

6. Functional Annotation (e.g., Disease Association Locus)

7. Chromatin ‘states’ annotate the regulatory genome Acknowledgements • HMM algorithm used to: • Learn dominant combinations or ‘states’ • Annotate genome by chromatin state in 1 cell type • Annotate genome by state dynamics in many cell types Heterochromatic State A -K4me2 -K27me3 -K36me3 +K9me3 Silencer State B -K4me2 +K27me3 -K36me3 +K9me3 Enhancer State C +K4me2 -K27me3 -K36me3 -K9me3 Ernst et al, In preparation

8. Example: Enhancer state in HepG2 implicates HNFs Acknowledgements “Enhancer” States “On” States “Off” State HNF1/3/4/6 show activator signatures in HepG2 cells Expression 2-2 22 HNF4 motif Fold enrichment 2-4 24

9. Chromatin accessibility maps reveal regulatory factor footprints Acknowledgements Th1 Neuronal (SKnSH) B-lymph. Hepatic (HepG2)

10. Individual and Population-level Variability Acknowledgements 6 Lymphoblastoid lines Approximately 5-10% of open chromatin regions display individual differences Children’s chromatin status are more like their parents

11. Profiling chromatin connectivity with 5C Acknowledgements Looping elements significantly enriched in insulators and enhancers 5C design: Identification of elements looping to TSSs Fold enrichment CTCF DHS H3K4Me1

12. 5C connects distal elements to their cognate gene(s) Acknowledgements 5C looping interaction α HS40 Alpha-globin CTCF ENCODE Chromatin & TF annotations

13. Publications Acknowledgements • ENCODE Chromatin Groups • Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2010; 7:47-49. • DNaseI Hypersensitivity at Gene-Poor, FSH Dystrophy-Linked 4q35.2. Proc. Nat’l Acad. Sci. USA in press (2010) • Kyle J. Gaulton, Takao Nammo, Lorenzo Pasquali, Jermy M. Simon, Paul G. Giresi, Marie P. Fogarty, Tami M. Panhuis, PiotrMieczkowski, Antonio Secchi, DomenicoBosco, Thierry Berney, Eduard Montonya, Karen L. Mohlke*, Jason D. Lieb*, and Jorge Ferrer*A map of open chromatin in human pancreatic islets. Nature Genetics, 42, 255-259 (2010) • Gheldof, N., Smith, E., Tabuchi, T., Koch, C., Dunham, I., Stamatoyannopoulos, J.A., Dekker, J. (2010). Cell type specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res. In press. • Ryan McDaniell, Bum-Kyu Lee, Lingyun Song, Zheng Liu, Alan P. Boyle, Michael R. Erdos, Laura J. Scott, Mario A Morken, Francis S. Collins, Katerina S. Kucera, Huntington Willard, Anna Battenhouse, Damian Keefe, Jason Lieb, Terrence S. Furey, Gregory E. Crawford, Vishwanath R. Iyer, and Ewan Birney. (2010) Individual-specific and allele-specific chromatin signatures in diverse human populations. Science in press (2010). • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Bernstein B, Bender M, Groudine M, Stamatoyannopoulos JA, Gnirke A, Mirny L, Lander ES, Dekker J. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326:289-93. • XueqingXu, Koji Tsumagari, Janet Sowden, Rabi Tawil, Alan P. Boyle, Lingyun Song, Terrence S. Furey, Gregory E. Crawford, and Melanie Ehrlich • Sekimata M, Pérez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, Dorschner MO, Stamatoyannopoulos JA*, Wilson CB. (2009). CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity, 31:551-64 • Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph SJ, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA*. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods, 6:283-9 • Boyle AP and Furey TS. High resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 1(2):319-329. (2009) • Hansen RS, Thomas S, Sandstrom R, Canfield T, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA*. (2009). Sequencing newly replicated DNA reveals widespread plasticity in human replication time. Proc. Nat’l Acad. Sci. USA, 107:139-44. • Dekker, J. (2008) Gene regulation in the third dimension. Science, 319(5871): 1793-1794. • Keys, J.R., Tallack, M.R., Zhan, Y., Papathanasiou, P., Goodnow, C.C., Gaensler, K.M., Crossley, M., Dekker, J. and Perkins, A.C. (2008) A mechanism for Ikaros regulation of human globin gene switching. Br. J. Haematol., 141(3): 398-406. • Miele, A. and Dekker, J. (2008) Long-range looping interactions and gene regulation. Mol. BioSyst., 4(11): 1046-1057. • D'haene, B., Attanasio, C., Beysen, D., Dostie, J., Lemire, E., Bouchard, Ph., Field, M., Jones, K., Lorenz, B., Menten, B., Buysse, K., Pattyn, F., Friedli, M., Ucla, C., Rossier, C., Wyss, C., Speleman, F., De Paepe, A., Dekker, J., Antonarakis, S.E. and De Baere, E. (2009) Disease-causing 7.4 kb cis-Regulatory deletion disrupting conserved non-coding sequences and their Interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet., 5 (6): e1000522. • Lajoie, B.R., van Berkum, N.L., Sanyal, A. and Dekker, J. (2009) My5C: web tools for chromosome conformation capture studies. Nat. Methods, 6(10): 690-691. • Alan P. Boyle, Sean Davis, Hennady P. Shulha, Elliott Margulies, Paul Meltzer, ZhipingWeng, Terrence S. Furey, Gregory E. Crawford High-resolution mapping and characterization of open chromatin across the genome. Cell, 132: 311-322. PMCID: PMC2669738(2008) • Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. FureyF-Seq: A Feature Density Estimator for High-Throughput Sequence Tags. Bioinformatics, doi: 10.1093/bioinformatics/btn480 (2008) • Data Users • Maeder, M.L., Thibodeau-Beganny, S., Osiak, A., Wright, D.A., Anthony, R.M., Eichtinger, M., Jiang, T., Foley, J.E., Winfrey, R.J., Townsend, J.A., et al. (2008). Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.Molecular Cell 31, 294-301. • Dong, X., Navratilova, P., Fredman, D., Drivenes, O., Becker, T.S., and Lenhard, B. (2009). Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.Nucleic Acids Research (Advanced Online) • Fujiwara, T., O'Geen, H., Keles, S., Blahnik, K., Linnemann, A.K., Kang, Y.A., Choi, K., Farnham, P.J., and Bresnick, E.H. (2009). Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy.Molecular Cell 36, 667-68 • Jiang, Y., Lucas, I., Young, D.J., Davis, E.M., Karrison, T., Rest, J.S., Le Beau, M.M. (2009). Common fragile sites are characterized by histonehypoacetylation.Human Mol Genet 18, 4501-4512.

14. Chromatin is integral for ENCODE Acknowledgements >103 • Promoters • Enhancers • Insulators • Transcripts • Silencers • TF Motifs • Binding • Regulation Power Chromatin Signatures Footprinting Assays State Dynamics TFs RNA Power Chromatin Cell types ~103