The goal of the ENCODE Project is to provide the biomedical community with a complete and biologically interpretable annotation of the human genome. This means discovering and mapping all parts of all genes, including exons, introns, promoters and cis-regulatory sequences, in previous phases of the ENCODE Project, the applicants of this proposal developed and applied robust, high-throughput, genome-wide methods for determining transcription factor occupancy, assessing DNA methylation, identifying RNA transcripts, and experimentally testing candidate regulatory elements and mutations. The combination of experiences from the previous phases with the resulting technology and analysis platforms and the existing, highly productive infrastructure of the applicants form the basis of this response to NHGRI's RFA-HG-11-024 ("Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms"). This application presents an ambitious proposal to expand the biological dimensions of ENCODE to include essentially all transcription factors for measurements of occupancy and to produce transcriptomes from hundreds of very specific cell types, and even single cells. The specific plan is to: 1) determine genome wide occupancy for all transcription factors and major cofactors with high resolution in two or more cell types;2) map and quantify all messenger RNA transcripts, microRNAs and other non-ribosomal RNAs in more than 300 well-defined, uncultured cell types;3) map DNA methylation state genome-wide at nucleotide resolution in more than 300 cell types;and 4) apply a high-throughput transient transfection assay system to test the impact of -2,000 candidate regulatory elements on gene regulation. All experimental work in this project will be evaluated by appropriate quality metrics, and after quality control, all data will be rapidly deposited in publi, freely accessible genome databases. In addition, computational analyses, including evaluation of comparative and population genomics data, will be integrated with the experimental production to help ensure quality and to capture information in forms useful to biologists, genomicists, and medical researchers. Completion of these Specific Aims will enable biomedical researchers to better and more rapidly understand the consequences of mutations in genomic disorders, including cancer, cardiovascular disease, and almost ail common diseases and, therefore, to more fully realize the potential of genomics to impact human health.

Public Health Relevance

Interpreting the human genome sequence remains a daunting challenge. We cannot yet recognize genes and their regulatory elements based solely on primary DNA sequence. This ambitious ENCODE Project proposal leverages new advances in genomic technologies to radically improve the depth, breadth, and analysis of functional element annotations of the human genome, accelerating the impact on human health by tying the effects of mutations in functional elements to the misregulation of gene expression in disease.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
1U54HG006998-01
Application #
8402461
Study Section
Special Emphasis Panel (ZHG1-HGR-M (M1))
Program Officer
Feingold, Elise A
Project Start
2012-09-21
Project End
2016-07-31
Budget Start
2012-09-21
Budget End
2013-07-31
Support Year
1
Fiscal Year
2012
Total Cost
$5,247,612
Indirect Cost
$976,488
Name
Hudson-Alpha Institute for Biotechnology
Department
Type
DUNS #
780007410
City
Huntsville
State
AL
Country
United States
Zip Code
35806
Hardison, Ross C (2016) A guide to translation of research results from model organisms to human. Genome Biol 17:161
Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A et al. (2016) Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 57:40-50
Han, G Celine; Vinayachandran, Vinesh; Bataille, Alain R et al. (2016) Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution. Mol Cell Biol 36:157-72
Polstein, Lauren R; Perez-Pinera, Pablo; Kocak, D Dewran et al. (2015) Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res 25:1158-69
Savic, Daniel; Roberts, Brian S; Carleton, Julia B et al. (2015) Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites. Genome Res 25:1791-800
Jain, Deepti; Mishra, Tejaswini; Giardine, Belinda M et al. (2015) Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system. Genom Data 4:1-7
Makova, Kateryna D; Hardison, Ross C (2015) The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet 16:213-23
Savic, Daniel; Partridge, E Christopher; Newberry, Kimberly M et al. (2015) CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins. Genome Res 25:1581-9
Dogan, Nergiz; Wu, Weisheng; Morrissey, Christapher S et al. (2015) Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 8:16
Marinov, Georgi K; Wang, Jie; Handler, Dominik et al. (2015) Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell 32:765-71

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