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Funk CC, Casella AM, Jung S, Richards MA, Rodriguez A, Shannon P, Donovan-Maiye R, Heavner B, Chard K, Xiao Y, Glusman G, Ertekin-Taner N, Golde TE, Toga A, Hood L, Van Horn JD, Kesselman C, Foster I, Madduri R, Price ND, Ament SA. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. Cell Rep 2021; 32:108029. [PMID: 32814038 DOI: 10.1016/j.celrep.2020.108029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 05/07/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022] Open
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.
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Affiliation(s)
- Cory C Funk
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alex M Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Medical Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Segun Jung
- Globus, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Ben Heavner
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Kyle Chard
- Globus, University of Chicago, Chicago, IL 60637, USA
| | - Yukai Xiao
- Globus, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Todd E Golde
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL 32224, USA
| | - Arthur Toga
- Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - John D Van Horn
- Department of Psychology, University of Southern California, Los Angeles, CA 90007, USA
| | - Carl Kesselman
- Information Sciences Institute, University of Southern California, Los Angeles, CA 90292, USA
| | - Ian Foster
- Globus, University of Chicago, Chicago, IL 60637, USA; Data Science and Learning Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ravi Madduri
- Globus, University of Chicago, Chicago, IL 60637, USA; Data Science and Learning Division, Argonne National Laboratory, Argonne, IL 60439, USA.
| | | | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Forrest MP, Zhang H, Moy W, McGowan H, Leites C, Dionisio LE, Xu Z, Shi J, Sanders AR, Greenleaf WJ, Cowan CA, Pang ZP, Gejman PV, Penzes P, Duan J. Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci. Cell Stem Cell 2017; 21:305-318.e8. [PMID: 28803920 PMCID: PMC5591074 DOI: 10.1016/j.stem.2017.07.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/25/2017] [Accepted: 07/13/2017] [Indexed: 01/12/2023]
Abstract
Most disease variants lie within noncoding genomic regions, making their functional interpretation challenging. Because chromatin openness strongly influences transcriptional activity, we hypothesized that cell-type-specific open chromatin regions (OCRs) might highlight disease-relevant noncoding sequences. To investigate, we mapped global OCRs in neurons differentiating from hiPSCs, a cellular model for studying neurodevelopmental disorders such as schizophrenia (SZ). We found that the OCRs are highly dynamic and can stratify GWAS-implicated SZ risk variants. Of the more than 3,500 SZ-associated variants analyzed, we prioritized ∼100 putatively functional ones located in neuronal OCRs, including rs1198588, at a leading risk locus flanking MIR137. Excitatory neurons derived from hiPSCs with CRISPR/Cas9-edited rs1198588 or a rare proximally located SZ risk variant showed altered MIR137 expression, dendrite arborization, and synapse maturation. Our study shows that noncoding disease variants in OCRs can affect neurodevelopment, and that analysis of open chromatin regions can help prioritize functionally relevant noncoding variants identified by GWAS.
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Affiliation(s)
- Marc P Forrest
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Winton Moy
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Heather McGowan
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Catherine Leites
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | | | - Zihui Xu
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | | | - Chad A Cowan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Pablo V Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Peter Penzes
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA.
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA.
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