A key goal in characterizing the human genome is to acquire a complete catalog of chromatin regulatory elements and sequence determinants of chromatin state. In this application, we propose to undertake a large-scale project to map the genomewide locations of >35 histone modifications and related proteins in >20 human cell types by coupling chromatin IP with massive-throughput sequencing on the Solexa platform. Our preliminary data demonstrate that this approach is highly accurate and a major advance over existing technologies in terms of cell requirements, genome coverage, throughput and cost-effectiveness. A sequencing pipeline will be applied to generate more than 500 genomewide datasets of chromatin structure by sequencing >1000 samples. A computational pipeline will then convert the sequencing reads into high resolution, genomewide maps that can be visualized in genome browsers and used for downstream analysis. Comparative genomic analysis and motif-finding tools will be applied to classify genomic sites based on associated chromatin structures and to identify underlying sequence determinants. Cell and molecular biology methods will be used to validate inferred functions for a representative subset of discovered elements. Chromatin regulation is extensively implicated in many aspects of human development and disease. In particular, cancer cells may universally exhibit aberrant chromatin states. The proposed systematic identification and characterization of chromatin regulatory elements in the human genome will offer unprecedented insight into the structure and function of chromatin, and provide an invaluable resource for investigators in chromatin, genomics, cancer and many other fields of research. All data collected in the context of the proposed project will be made available pre-publication to the greater scientific community once reliability has been confirmed.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
3U54HG004570-04S2
Application #
8321257
Study Section
Special Emphasis Panel (ZHG1-HGR-M (O1))
Program Officer
Feingold, Elise A
Project Start
2007-09-28
Project End
2013-06-30
Budget Start
2011-07-01
Budget End
2013-06-30
Support Year
4
Fiscal Year
2011
Total Cost
$339,000
Indirect Cost
Name
Broad Institute, Inc.
Department
Type
DUNS #
623544785
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Ernst, Jason; Kellis, Manolis (2017) Chromatin-state discovery and genome annotation with ChromHMM. Nat Protoc 12:2478-2492
Ryan, Russell J H; Petrovic, Jelena; Rausch, Dylan M et al. (2017) A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep 21:784-797
van Galen, Peter; Viny, Aaron D; Ram, Oren et al. (2016) A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell 61:170-80
Ryan, Russell J H; Drier, Yotam; Whitton, Holly et al. (2015) Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov 5:1058-71
Ernst, Jason; Kellis, Manolis (2015) Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat Biotechnol 33:364-76
Yen, Angela; Kellis, Manolis (2015) Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. Nat Commun 6:7973
Farh, Kyle Kai-How; Marson, Alexander; Zhu, Jiang et al. (2015) Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518:337-43
Riggi, Nicolò; Knoechel, Birgit; Gillespie, Shawn M et al. (2014) EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 26:668-681
Yashiro-Ohtani, Yumi; Wang, Hongfang; Zang, Chongzhi et al. (2014) Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A 111:E4946-53
Knoechel, Birgit; Roderick, Justine E; Williamson, Kaylyn E et al. (2014) An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet 46:364-70

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