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 Fisher; Nir Friedmann; Bang Wong; Bradley E. Bernstein; Chad Nusbaum; Nir Hacohen; Aviv Regev; Ido Amit

doi:10.1016/j.molcel.2012.07.030

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 Friedmann, Bang Wong, Bradley E. Bernstein, Chad Nusbaum, Nir Hacohen, Aviv Regev, Ido Amit^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

298 Citations (Scopus)

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 language	English
Pages (from-to)	810-822
Number of pages	13
Journal	Molecular Cell
Volume	47
Issue number	5
DOIs	https://doi.org/10.1016/j.molcel.2012.07.030
Publication status	Published - 14 Sept 2012

Funding

Human Frontiers Science Program; Career Development Award; ISF; Bikura Institutional Research Grant Program; ERC [309788]; Broad Institute; DARPA [D12AP00004]; HHMI, NHGRI [1P01HG005062-01]; NIH PIONEER award [DP1-OD003958-01]; Burroughs-Wellcome Fund Career Award at the Scientific Interface; Center for Excellence in Genome Science from the NHGRI [1P50HG006193]; EU; US-Israel Binational Science Foundation; New England Regional Center for Excellence/Biodefense and Emerging Infectious Disease [U54 AI057159]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.)

All Science Journal Classification (ASJC) codes

Molecular Biology
Cell Biology

Access to Document

10.1016/j.molcel.2012.07.030Licence: Unspecified

Cite this

Garber, M., Yosef, N., Goren, A., Raychowdhury, R., Thielke, A., Guttman, M., Robinson, J., Minie, B., Chevrier, N., Itzhaki, Z., Blecher-Gonen, R., Bornstein, C., Amann Zalcenstein, D., Weiner, A., Friedrich, D., Meldrim, J., Ram, O., Cheng, C., Gnirke, A., ... Amit, I. (2012). A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals. Molecular Cell, 47(5), 810-822. https://doi.org/10.1016/j.molcel.2012.07.030

@article{b18ce99a875d42bc9a3e3a235e2fbb49,

title = "A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals",

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.",

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

year = "2012",

month = sep,

day = "14",

doi = "10.1016/j.molcel.2012.07.030",

language = "English",

volume = "47",

pages = "810--822",

journal = "Molecular Cell",

issn = "1097-2765",

publisher = "Cell Press",

number = "5",

}

Garber, M, Yosef, N, Goren, A, Raychowdhury, R, Thielke, A, Guttman, M, Robinson, J, Minie, B, Chevrier, N, Itzhaki, Z, Blecher-Gonen, R, Bornstein, C, Amann Zalcenstein, D, Weiner, A, Friedrich, D, Meldrim, J, Ram, O, Cheng, C, Gnirke, A, Fisher, S, Friedmann, N, Wong, B, Bernstein, BE, Nusbaum, C, Hacohen, N, Regev, A & Amit, I 2012, 'A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals', Molecular Cell, vol. 47, no. 5, pp. 810-822. https://doi.org/10.1016/j.molcel.2012.07.030

TY - JOUR

T1 - A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

AU - Garber, Manuel

AU - Yosef, Nir

AU - Goren, Alon

AU - Raychowdhury, Raktima

AU - Thielke, Anne

AU - Guttman, Mitchell

AU - Robinson, James

AU - Minie, Brian

AU - Chevrier, Nicolas

AU - Itzhaki, Zohar

AU - Blecher-Gonen, Ronnie

AU - Bornstein, Chamutal

AU - Amann Zalcenstein, Daniela

AU - Weiner, Assaf

AU - Friedrich, Dennis

AU - Meldrim, James

AU - Ram, Oren

AU - Cheng, Christine

AU - Gnirke, Andreas

AU - Fisher, Sheila

AU - Friedmann, Nir

AU - Wong, Bang

AU - Bernstein, Bradley E.

AU - Nusbaum, Chad

AU - Hacohen, Nir

AU - Regev, Aviv

AU - Amit, Ido

PY - 2012/9/14

Y1 - 2012/9/14

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84866303839&partnerID=8YFLogxK

U2 - 10.1016/j.molcel.2012.07.030

DO - 10.1016/j.molcel.2012.07.030

M3 - Article

C2 - 22940246

SN - 1097-2765

VL - 47

SP - 810

EP - 822

JO - Molecular Cell

JF - Molecular Cell

IS - 5

ER -

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

Abstract

Funding

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this