ENCODE Participants and Projects

• Production Scale Effort
• Mouse ENCODE Production Scale Effort
• Pilot Scale Effort
• Data Coordination Center
• Data Analysis Center
• Technology Development Effort

ENCODE Production Scale Effort

Research Group Institution Research Goals Bradley Bernstein Broad Institute of MIT and Harvard Map histone modifications using chromatin immunoprecipitation followed by high-throughput sequencing. Gregory Crawford Duke University Identify and characterize regions of open chromatin using DNaseI hypersensitivity assays, formaldehyde-assisted isolation of regulatory elements, and chromatin immunoprecipitation. Morgan Giddings University of North Carolina, Chapel Hill Produce large-scale proteomic data sets on ENCODE cell lines using mass spectrometry. Thomas Gingeras Affymetrix, Inc. Identify protein-coding and non-protein coding RNA transcripts using microarrays, high-throughput sequencing, sequence paired-end tags, and sequenced cap analysis of gene expression tags. Timothy Hubbard Wellcome Trust Sanger Institute Annotate gene features using computational methods, manual annotation, and targeted experiments. Richard Myers HudsonAlpha Institute for Biotechnology Identify transcription factor binding sites using chromatin immunoprecipitation followed by high-throughput DNA sequencing; Pilot effort to determine the methylation status of CpG-rich regions. Michael Snyder Stanford University Identify transcription factor binding sites using chromatin immunoprecipitation followed by high-throughput DNA sequencing. John Stamatoyannopoulos University of Washington, Seattle Map and functionally classify DNaseI hypersensitive sites by digital DNaseI and histone modification mapping using high-throughput sequencing. Thomas Tullius Boston University Develop high-throughput methods for collecting hydroxyl radical cleavage data; locate structural features in human genome that are under selective evolutionary pressure, but for which the exact nucleotide sequence is not under selection. Kevin White University of Chicago Epitope tag transcription factors for chromatin immunoprecipitation using BAC recombineering.

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Mouse ENCODE Production Scale Effort

Research Group	Institution	Goals
Ross Hardison	Pennsylvania State University	Identify molecular events retained by both mouse and human since divergence using genome-wide assays; analyze how conservation of biochemical features relates to conservation of DNA sequence and conservation of regulated gene expression.
Bing Ren	Ludwig Institute for Cancer Research	Conduct a genome-wide analysis of active promoters, enhancers and insulator elements in embryonic and adult mouse tissue using high throughput experimental strategy.
Michael Snyder	Stanford University	Map the binding sites of transcription factors in mouse cell lines orthologous to well-studied human cell lines.
John Stamatoyannopoulos	University of Washington, Seattle	Produce comprehensive maps of mouse regulatory DNA marked by DNaseI hypersensitive sites using ultra-deep sequencing.

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ENCODE Pilot Scale Effort

Research Group Institution Research Goals Job Dekker University of Massachusetts Medical School Map long-range gene regulatory elements using 5C (Chromosome Conformation Capture carbon-copy) Laura Elnitski National Human Genome Research Institute Map silencer and enhancer blocker elements using transient transfection assays; Study bidirectional promoters that map across species. Eric Green National Human Genome Research Institute Generate and analyze BAC-based sequence data. Elliott Margulies National Human Genome Research Institute Develop and implement analytical methods for identifying and characterizing evolutionarily constrained sequences. Scott Tenenbaum University at Albany-State University of New York Identify sites that are targets for RNA-binding proteins using immunoprecipitation followed by microarrays or high-throughput sequencing. Zhiping Weng University of Massachusetts Medical School Predict transcription factor binding sites that determine active promoters using computational methods.

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ENCODE Data Coordination Center

Research Group Institution Research Goals W. James Kent University of California, Santa Cruz Collect, organize, store, manage, and provide access to data from ENCODE and related projects

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ENCODE Data Analysis Center

Research Group Institution Research Goals Ewan Birney European Bioinformatics Institute Coordinate and assist in the integrative analysis of data produced by the ENCODE Consortium

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ENCODE Technology Development Effort

Research Group Institution Research Goals Howard Chang Stanford University Develop high-throughput methods to predict functional motifs in RNA, to map RNA structure, and to assign biological functions to RNA motifs. Michael Dorschner University of Washington, Seattle Develop an in vivo method for identifying sites of protein-DNA interaction using cleavage sensitivity with UV light, dimethylsulfate, and DNaseI followed by single molecule sequencing. John Greally Albert Einstein College of Medicine Develop high-throughput methods to analyze cytosine methylation and map histone modifications. Xiaoman Li University of Central Florida Develop computational methods for identifying conserved cis-regulatory modules in non-protein coding regions. Marcelo Nobrega University of Chicago Develop tagged DNA binding proteins that are recognizable by tag-specific antibodies; Develop platforms to test predicted enhancers, silencers and insulators. Yijun Ruan Genome Institute of Singapore Develop methods that use high-throughput sequencing to characterize long-range chromatin interactions involved in transcription.

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Last Reviewed: May 21, 2012