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Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.
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- Additional Information
- Source:
Publisher: Cell Press Country of Publication: United States NLM ID: 101573691 Publication Model: Print Cited Medium: Internet ISSN: 2211-1247 (Electronic) NLM ISO Abbreviation: Cell Rep Subsets: MEDLINE
- Publication Information:
Original Publication: [Cambridge, MA] : Cell Press, c 2012-
- Subject Terms:
- Abstract:
Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.
Competing Interests: Declaration of Interests The authors declare no competing interests.
(Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
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- Grant Information:
U54 EB020406 United States EB NIBIB NIH HHS; R24 MH114815 United States MH NIMH NIH HHS; RF1 AG051504 United States AG NIA NIH HHS; R01 AG061796 United States AG NIA NIH HHS; U01 AG046139 United States AG NIA NIH HHS; P30 AG062677 United States AG NIA NIH HHS; F30 MH120910 United States MH NIMH NIH HHS; R24 MH114788 United States MH NIMH NIH HHS; R01 HG009018 United States HG NHGRI NIH HHS; P50 GM076547 United States GM NIGMS NIH HHS; RF1 AG057443 United States AG NIA NIH HHS
- Contributed Indexing:
Keywords: DNase-seq; ENCODE; footprinting; gene regulation; motifs; psychiatric genetics; transcription factors
- Accession Number:
0 (Transcription Factors)
EC 3.1.- (Deoxyribonucleases)
- Publication Date:
Date Created: 20200820 Date Completed: 20210528 Latest Revision: 20240801
- Publication Date:
20240801
- Accession Number:
PMC7462736
- Accession Number:
10.1016/j.celrep.2020.108029
- Accession Number:
32814038
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