A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

Manuel Garber*, Nir Yosef, Alon Goren, Raktima Raychowdhury, Anne Thielke, Mitchell Guttman, James Robinson, Brian Minie, Nicolas Chevrier, Zohar Itzhaki, Ronnie Blecher-Gonen, Chamutal Bornstein, Daniela Amann-Zalcenstein, Assaf Weiner, Dennis Friedrich, James Meldrim, Oren Ram, Christine Cheng, Andreas Gnirke, Sheila FisherNir Friedman, Bang Wong, Bradley E. Bernstein, Chad Nusbaum, Nir Hacohen, Aviv Regev, Ido Amit

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

294 Scopus citations

Abstract

Understanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen stimulus of dendritic cells. Analyzing over 180,000 TF-DNA interactions we find that TFs vary substantially in their temporal binding landscapes. This data suggests a model for transcription regulation whereby TF networks are hierarchically organized into cell differentiation factors, factors that bind targets prior to stimulus to prime them for induction, and factors that regulate specific gene programs. Overlaying HT-ChIP data on gene-expression dynamics shows that many TF-DNA interactions are established prior to the stimuli, predominantly at immediate-early genes, and identified specific TF ensembles that coordinately regulate gene-induction.

Original languageAmerican English
Pages (from-to)810-822
Number of pages13
JournalMolecular Cell
Volume47
Issue number5
DOIs
StatePublished - 14 Sep 2012

Bibliographical note

Funding Information:
We thank Schraga Schwartz, Tommy Kaplan, Ami Citri, Kevin Struhl, Gioacchino Natoli, Richard Young, and John Rinn for valuable discussions and comments; Leslie Gaffney for artwork; Jim Bochicchio for project management; and the Broad Sequencing Platform. This project was supported by the Human Frontiers Science Program; Career Development Award; an ISF; Bikura Institutional Research Grant Program; ERC starting grant 309788 (I.A.); by the Broad Institute (M.G., N.Y., I.A., A.R.); and by DARPA D12AP00004 (M.G.). HHMI, NHGRI grant 1P01HG005062-01; an NIH PIONEER award DP1-OD003958-01; a Burroughs-Wellcome Fund Career Award at the Scientific Interface; and a Center for Excellence in Genome Science from the NHGRI 1P50HG006193 (A.R.); A.R. is a fellow of the Merkin Foundation for Stem Cell Research at the Broad Institute and by the New England Regional Center for Excellence/Biodefense and Emerging Infectious Disease U54 AI057159 (N.H.). EU FP7 Model-In (N.F.) and US-Israel Binational Science Foundation (N.F. and A.R.)

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