1. A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals
- Author
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Christine S. Cheng, Oren Ram, Brian Minie, Dennis C. Friedrich, Daniela Amann-Zalcenstein, Alon Goren, Chamutal Bornstein, James T. Robinson, Bang Wong, Mitchell Guttman, Andreas Gnirke, Sheila Fisher, Anne Thielke, Zohar Itzhaki, Assaf Weiner, Nir Yosef, James Meldrim, Ronnie Blecher-Gonen, Nir Friedman, Nir Hacohen, Raktima Raychowdhury, Bradley E. Bernstein, Manuel Garber, Ido Amit, Nicolas Chevrier, Aviv Regev, and Chad Nusbaum
- Subjects
Chromatin Immunoprecipitation ,Computational biology ,Biology ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Transcriptional regulation ,Animals ,Molecular Biology ,Transcription factor ,ChIA-PET ,030304 developmental biology ,Genetics ,Regulation of gene expression ,0303 health sciences ,Cell Biology ,DNA ,Dendritic Cells ,ChIP-on-chip ,Chromatin ,ChIP-sequencing ,High-Throughput Screening Assays ,Gene Expression Regulation ,Chromatin immunoprecipitation ,030217 neurology & neurosurgery ,Transcription Factors - 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.
- Published
- 2012