Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Logo for

Science 326 (5950): 257-263

Copyright © 2009 by the American Association for the Advancement of Science

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Ido Amit,1,2,3,4 Manuel Garber,1,* Nicolas Chevrier,2,3,* Ana Paula Leite,1,5,* Yoni Donner,1,* Thomas Eisenhaure,2,3 Mitchell Guttman,1,4 Jennifer K. Grenier,1 Weibo Li,2,3 Or Zuk,1 Lisa A. Schubert,6 Brian Birditt,6 Tal Shay,1 Alon Goren,1,7 Xiaolan Zhang,1 Zachary Smith,1 Raquel Deering,2,3 Rebecca C. McDonald,2,3 Moran Cabili,1 Bradley E. Bernstein,1,3,7 John L. Rinn,1 Alex Meissner,1 David E. Root,1 Nir Hacohen,1,2,3,{dagger},{ddagger} Aviv Regev1,4,8,{ddagger}

Abstract: Models of mammalian regulatory networks controlling gene expression have been inferred from genomic data but have largely not been validated. We present an unbiased strategy to systematically perturb candidate regulators and monitor cellular transcriptional responses. We applied this approach to derive regulatory networks that control the transcriptional response of mouse primary dendritic cells to pathogens. Our approach revealed the regulatory functions of 125 transcription factors, chromatin modifiers, and RNA binding proteins, which enabled the construction of a network model consisting of 24 core regulators and 76 fine-tuners that help to explain how pathogen-sensing pathways achieve specificity. This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells.

1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
2 Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA.
3 Harvard Medical School, Boston, MA 02115, USA.
4 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
5 Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
6 NanoString Technologies, 530 Fairview Avenue N., Suite 2000, Seattle, WA 98109, USA.
7 Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA.
8 Howard Hughes Medical Institute.

* These authors contributed equally to this work.

{ddagger} These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: nhacohen{at}

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli.
A. Zeisel, W. J. Kostler, N. Molotski, J. M. Tsai, R. Krauthgamer, J. Jacob-Hirsch, G. Rechavi, Y. Soen, S. Jung, Y. Yarden, et al. (2014)
Mol Syst Biol 7, 529
   Abstract »    Full Text »    PDF »
Environmental and genetic perturbations reveal different networks of metabolic regulation.
A. J. Greenberg, S. R. Hackett, L. G. Harshman, and A. G. Clark (2014)
Mol Syst Biol 7, 563
   Abstract »    Full Text »    PDF »
The phosphoproteome of toll-like receptor-activated macrophages.
G. Weintz, J. V. Olsen, K. Fruhauf, M. Niedzielska, I. Amit, J. Jantsch, J. Mages, C. Frech, L. Dolken, M. Mann, et al. (2014)
Mol Syst Biol 6, 371
   Abstract »    Full Text »    PDF »
Digital cell quantification identifies global immune cell dynamics during influenza infection.
Z. Altboum, Y. Steuerman, E. David, Z. Barnett-Itzhaki, L. Valadarsky, H. Keren-Shaul, T. Meningher, E. Mendelson, M. Mandelboim, I. Gat-Viks, et al. (2014)
Mol Syst Biol 10, 720
   Abstract »    Full Text »    PDF »
Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types.
D. A. Jaitin, E. Kenigsberg, H. Keren-Shaul, N. Elefant, F. Paul, I. Zaretsky, A. Mildner, N. Cohen, S. Jung, A. Tanay, et al. (2014)
Science 343, 776-779
   Abstract »    Full Text »    PDF »
Functional genomics of the inflammatory response: where are we now?.
M. Simonatto and G. Natoli (2013)
Briefings in Functional Genomics 12, 483-488
   Abstract »    Full Text »    PDF »
Higher Expression of Several Interferon-Stimulated Genes in HIV-1-Infected Females After Adjusting for the Level of Viral Replication.
J. J. Chang, M. Woods, R. J. Lindsay, E. H. Doyle, M. Griesbeck, E. S. Chan, G. K. Robbins, R. J. Bosch, and M. Altfeld (2013)
The Journal of Infectious Disease 208, 830-838
   Abstract »    Full Text »    PDF »
Aryl Hydrocarbon Receptor Control of Adaptive Immunity.
F. J. Quintana and D. H. Sherr (2013)
Pharmacol. Rev. 65, 1148-1161
   Abstract »    Full Text »    PDF »
The Emerging Field of Human Social Genomics.
G. M. Slavich and S. W. Cole (2013)
Clinical Psychological Science 1, 331-348
   Abstract »    Full Text »    PDF »
Toll-Like Receptor 7 Inhibits Early Acute Retroviral Infection through Rapid Lymphocyte Responses.
E. P. Browne (2013)
J. Virol. 87, 7357-7366
   Abstract »    Full Text »    PDF »
ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens.
D. D. Shao, A. Tsherniak, S. Gopal, B. A. Weir, P. Tamayo, N. Stransky, S. E. Schumacher, T. I. Zack, R. Beroukhim, L. A. Garraway, et al. (2013)
Genome Res. 23, 665-678
   Abstract »    Full Text »    PDF »
An Evolutionarily Conserved Innate Immunity Protein Interaction Network.
L. De Arras, A. Seng, B. Lackford, M. R. Keikhaee, B. Bowerman, J. H. Freedman, D. A. Schwartz, and S. Alper (2013)
J. Biol. Chem. 288, 1967-1978
   Abstract »    Full Text »    PDF »
Integrative genomic analysis of the human immune response to influenza vaccination.
L. M. Franco, K. L. Bucasas, J. M. Wells, D. Nino, X. Wang, G. E. Zapata, N. Arden, A. Renwick, P. Yu, J. M. Quarles, et al. (2013)
eLife Sci 2, e00299
   Abstract »    Full Text »    PDF »
miR-451 Regulates Dendritic Cell Cytokine Responses to Influenza Infection.
C. M. Rosenberger, R. L. Podyminogin, G. Navarro, G.-W. Zhao, P. S. Askovich, M. J. Weiss, and A. Aderem (2012)
J. Immunol. 189, 5965-5975
   Abstract »    Full Text »    PDF »
Polymorphisms in Toll-Like Receptor 4 Underlie Susceptibility to Tumor Induction by the Mouse Polyomavirus.
P. Velupillai, C. K. Sung, E. Andrews, J. Moran, D. Beier, J. Kagan, and T. Benjamin (2012)
J. Virol. 86, 11541-11547
   Abstract »    Full Text »    PDF »
Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages.
X. Chen, I. Barozzi, A. Termanini, E. Prosperini, A. Recchiuti, J. Dalli, F. Mietton, G. Matteoli, S. Hiebert, and G. Natoli (2012)
PNAS 109, E2865-E2874
   Abstract »    Full Text »    PDF »
Activation of type I interferon-dependent genes characterizes the "core response" induced by CpG DNA.
F. Steinhagen, C. Meyer, D. Tross, M. Gursel, T. Maeda, S. Klaschik, and D. M. Klinman (2012)
J. Leukoc. Biol. 92, 775-785
   Abstract »    Full Text »    PDF »
EHMT1 Protein Binds to Nuclear Factor-{kappa}B p50 and Represses Gene Expression.
C.-K. Ea, S. Hao, K. S. Yeo, and D. Baltimore (2012)
J. Biol. Chem. 287, 31207-31217
   Abstract »    Full Text »    PDF »
Plenary Perspective: The complexity of constitutive and inducible gene expression in mononuclear phagocytes.
D. A. Hume (2012)
J. Leukoc. Biol. 92, 433-444
   Abstract »    Full Text »    PDF »
Identification of aberrant pathways and network activities from high-throughput data.
J. Wang, Y. Zhang, C. Marian, and H. W. Ressom (2012)
Brief Bioinform 13, 406-419
   Abstract »    Full Text »    PDF »
Genomics and Bioinformatics of Parkinson's Disease.
S. W. Scholz, T. Mhyre, H. Ressom, S. Shah, and H. J. Federoff (2012)
Cold Spring Harb Perspect Med 2, a009449
   Abstract »    Full Text »    PDF »
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
K. Schroder, K. M. Irvine, M. S. Taylor, N. J. Bokil, K.-A. Le Cao, K.-A. Masterman, L. I. Labzin, C. A. Semple, R. Kapetanovic, L. Fairbairn, et al. (2012)
PNAS 109, E944-E953
   Abstract »    Full Text »    PDF »
Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells.
S. Kubicek, J. C. Gilbert, D. Fomina-Yadlin, A. D. Gitlin, Y. Yuan, F. F. Wagner, E. B. Holson, T. Luo, T. A. Lewis, B. Taylor, et al. (2012)
PNAS 109, 5364-5369
   Abstract »    Full Text »    PDF »
Host Genes Important to HIV Replication and Evolution.
A. Telenti and W. E. Johnson (2012)
Cold Spring Harb Perspect Med 2, a007203
   Abstract »    Full Text »    PDF »
Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery.
H. Li, H. Zhou, D. Wang, J. Qiu, Y. Zhou, X. Li, M. G. Rosenfeld, S. Ding, and X.-D. Fu (2012)
PNAS 109, 4609-4614
   Abstract »    Full Text »    PDF »
On a fundamental structure of gene networks in living cells.
N. Kravchenko-Balasha, A. Levitzki, A. Goldstein, V. Rotter, A. Gross, F. Remacle, and R. D. Levine (2012)
PNAS 109, 4702-4707
   Abstract »    Full Text »    PDF »
Learning vaccinology from viral infections.
R. Ahmed and B. Pulendran (2011)
J. Exp. Med. 208, 2347-2349
   Abstract »    Full Text »    PDF »
Synthetic double-stranded RNA induces innate immune responses similar to a live viral vaccine in humans.
M. Caskey, F. Lefebvre, A. Filali-Mouhim, M. J. Cameron, J.-P. Goulet, E. K. Haddad, G. Breton, C. Trumpfheller, S. Pollak, I. Shimeliovich, et al. (2011)
J. Exp. Med. 208, 2357-2366
   Abstract »    Full Text »    PDF »
Epigenetics, bioenergetics, and microRNA coordinate gene-specific reprogramming during acute systemic inflammation.
C. E. McCall, M. El Gazzar, T. Liu, V. Vachharajani, and B. Yoza (2011)
J. Leukoc. Biol. 90, 439-446
   Abstract »    Full Text »    PDF »
Drosophila RNAi screening in a postgenomic world.
C. Bakal (2011)
Briefings in Functional Genomics
   Abstract »    Full Text »    PDF »
The Ectodomain of the Toll-like Receptor 4 Prevents Constitutive Receptor Activation.
G. Panter and R. Jerala (2011)
J. Biol. Chem. 286, 23334-23344
   Abstract »    Full Text »    PDF »
Physical Module Networks: an integrative approach for reconstructing transcription regulation.
N. Novershtern, A. Regev, and N. Friedman (2011)
Bioinformatics 27, i177-i185
   Abstract »    Full Text »    PDF »
An integrative clustering and modeling algorithm for dynamical gene expression data.
J. Sivriver, N. Habib, and N. Friedman (2011)
Bioinformatics 27, i392-i400
   Abstract »    Full Text »    PDF »
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.
A. Lan, I. Y. Smoly, G. Rapaport, S. Lindquist, E. Fraenkel, and E. Yeger-Lotem (2011)
Nucleic Acids Res. 39, W424-W429
   Abstract »    Full Text »    PDF »
Herpes Simplex Virus Type 1-Induced Transcriptional Networks of Corneal Endothelial Cells Indicate Antigen Presentation Function.
D. Miyazaki, T. Haruki, S. Takeda, S.-i. Sasaki, K. Yakura, Y. Terasaka, N. Komatsu, S. Yamagami, H. Touge, C. Touge, et al. (2011)
Invest. Ophthalmol. Vis. Sci. 52, 4282-4293
   Abstract »    Full Text »    PDF »
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression.
L. T. MacNeil and A. J. M. Walhout (2011)
Genome Res. 21, 645-657
   Abstract »    Full Text »    PDF »
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
R. Pique-Regi, J. F. Degner, A. A. Pai, D. J. Gaffney, Y. Gilad, and J. K. Pritchard (2011)
Genome Res. 21, 447-455
   Abstract »    Full Text »    PDF »
The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF-{kappa}B p50.
C. S. Cheng, K. E. Feldman, J. Lee, S. Verma, D.-B. Huang, K. Huynh, M. Chang, J. V. Ponomarenko, S.-C. Sun, C. A. Benedict, et al. (2011)
Science Signaling 4, ra11
   Abstract »    Full Text »    PDF »
The genomic landscapes of inflammation.
G. Natoli, S. Ghisletti, and I. Barozzi (2011)
Genes & Dev. 25, 101-106
   Abstract »    Full Text »    PDF »
Beyond the enhanceosome: cluster of novel {kappa}B sites downstream of the human IFN-{beta} gene is essential for lipopolysaccharide-induced gene activation.
F. G. Goh, S. J. P. Thomson, T. Krausgruber, A. Lanfrancotti, R. R. Copley, and I. A. Udalova (2010)
Blood 116, 5580-5588
   Abstract »    Full Text »    PDF »
Digital Gene Expression Signatures for Maize Development.
A. L. Eveland, N. Satoh-Nagasawa, A. Goldshmidt, S. Meyer, M. Beatty, H. Sakai, D. Ware, and D. Jackson (2010)
Plant Physiology 154, 1024-1039
   Abstract »    Full Text »    PDF »
Genomic Approaches to the Study of HIV-1 Acquisition.
A. Telenti and P. McLaren (2010)
The Journal of Infectious Disease 202, S382-s386
   Abstract »    Full Text »    PDF »
Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes.
L. G. Alexopoulos, J. Saez-Rodriguez, B. D. Cosgrove, D. A. Lauffenburger, and P. K. Sorger (2010)
Mol. Cell. Proteomics 9, 1849-1865
   Abstract »    Full Text »    PDF » a resource for systematic discovery of transcription factor target genes.
S. M. Kielbasa, N. Bluthgen, M. Fahling, and R. Mrowka (2010)
Nucleic Acids Res. 38, W233-W238
   Abstract »    Full Text »    PDF »
2009: Signaling Breakthroughs of the Year.
E. M. Adler (2010)
Science Signaling 3, eg1
   Abstract »    Full Text »    PDF »
Toward a Systems-Level Analysis of Infection Biology: A New Method for Conducting Genetic Screens in Human Cells.
S. A. Stanley and D. T. Hung (2009)
Science Translational Medicine 1, 11ps13
   Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882