A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

Cell

Volumn 165, Issue 1, 2016, Pages 165-179

  Tong, Ann Jay ^a   Liu, Xin ^a   Thomas, Brandon J ^a   Lissner, Michelle M ^a   Baker, Mairead R ^b   Senagolage, Madhavi D ^b   Allred, Amanda L ^b   Barish, Grant D ^b   Smale, Stephen T ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LIPID A; TRANSCRIPTION FACTOR; ALPHA BETA INTERFERON RECEPTOR; SERUM RESPONSE FACTOR;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BONE MARROW DERIVED MACROPHAGE; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; INFLAMMATION; MACROPHAGE; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; RNA SEQUENCE; ANIMAL; C57BL MOUSE; GENE REGULATORY NETWORK; GENETICS; IMMUNOLOGY; METABOLISM;

ANIMALS; GENE REGULATORY NETWORKS; INFLAMMATION; LIPID A; MACROPHAGES; MICE; MICE, INBRED C57BL; NF-KAPPA B; RECEPTOR, INTERFERON ALPHA-BETA; SERUM RESPONSE FACTOR;

EID: 84975784410     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.01.020     Document Type: Article

References (32)

1. T. Agalioti, S. Lomvardas, B. Parekh, J. Yie, T. Maniatis, and D. Thanos Ordered recruitment of chromatin modifying and general transcription factors to the IFN-β promoter Cell 103 2000 667 678
2. I. Amit, M. Garber, N. Chevrier, A.P. Leite, Y. Donner, T. Eisenhaure, M. Guttman, J.K. Grenier, W. Li, O. Zuk, and et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses Science 326 2009 257 263
3. G.D. Barish, R.T. Yu, M. Karunasiri, C.B. Ocampo, J. Dixon, C. Benner, A.L. Dent, R.K. Tangirala, and R.M. Evans Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response Genes Dev. 24 2010 2760 2765
4. Y. Benjamini, and Y. Hochberg Controlling the false discovery rate: A practical and powerful approach to multiple testing J.R. Stat. Soc. 57 1995 289 300
5. D.M. Bhatt, A. Pandya-Jones, A.J. Tong, I. Barozzi, M.M. Lissner, G. Natoli, D.L. Black, and S.T. Smale Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions Cell 150 2012 279 290
6. J.D. Buenrostro, B. Wu, H.Y. Chang, and W.J. Greenleaf ATAC-seq: A method for assaying chromatin accessibility genome-wide Curr. Protoc. Mol. Biol. 109 2015 21.29.1-21.29.9
7. L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
8. J.E. Freaney, R. Kim, R. Mandhana, and C.M. Horvath Extensive cooperation of immune master regulators IRF3 and NFκB in RNA Pol II recruitment and pause release in human innate antiviral transcription Cell Rep. 4 2013 959 973
9. M. Garber, N. Yosef, A. Goren, R. Raychowdhury, A. Thielke, M. Guttman, J. Robinson, B. Minie, N. Chevrier, Z. Itzhaki, and et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals Mol. Cell 47 2012 810 822
10. S. Ghisletti, I. Barozzi, F. Mietton, S. Polletti, F. De Santa, E. Venturini, L. Gregory, L. Lonie, A. Chew, C.-L. Wei, and et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages Immunity 32 2010 317 328
11. D.C. Hargreaves, T. Horng, and R. Medzhitov Control of inducible gene expression by signal-dependent transcriptional elongation Cell 138 2009 129 145
12. S. Heinz, C. Benner, N. Spann, E. Bertolino, Y.C. Lin, P. Laslo, J.X. Cheng, C. Murre, H. Singh, and C.K. Glass Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities Mol. Cell 38 2010 576 589
13. J.C. Kagan, T. Su, T. Horng, A. Chow, S. Akira, and R. Medzhitov TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-beta Nat. Immunol. 9 2008 361 368
14. T.I. Lee, S.E. Johnstone, and R.A. Young Chromatin immunoprecipitation and microarray-based analysis of protein location Nat. Protoc. 1 2006 729 748
15. J.Z. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D.A. Thompson, N. Friedman, A. Gnirke, and A. Regev Comprehensive comparative analysis of strand-specific RNA sequencing methods Nat. Methods 7 2010 709 715
16. C.-A. Lim, F. Yao, J.J.-Y. Wong, J. George, H. Xu, K.P. Chiu, W.-K. Sung, L. Lipovich, V.B. Vega, J. Chen, and et al. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation Mol. Cell 27 2007 622 635
17. J.C. Marioni, C.E. Mason, S.M. Mane, M. Stephens, and Y. Gilad RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays Genome Res. 18 2008 1509 1517
18. R. Martone, G. Euskirchen, P. Bertone, S. Hartman, T.E. Royce, N.M. Luscombe, J.L. Rinn, F.K. Nelson, P. Miller, M. Gerstein, and et al. Distribution of NF-kappaB-binding sites across human chromosome 22 Proc. Natl. Acad. Sci. USA 100 2003 12247 12252
19. S.M. Metcalfe LIF in the regulation of T-cell fate and as a potential therapeutic Genes Immun. 12 2011 157 168
20. R. Ostuni, V. Piccolo, I. Barozzi, S. Polletti, A. Termanini, S. Bonifacio, A. Curina, E. Prosperini, S. Ghisletti, and G. Natoli Latent enhancers activated by stimulation in differentiated cells Cell 152 2013 157 171
21. D. Panne, T. Maniatis, and S.C. Harrison An atomic model of the interferon-beta enhanceosome Cell 129 2007 1111 1123
22. G. Posern, and R. Treisman Actin' together: Serum response factor, its cofactors and the link to signal transduction Trends Cell Biol. 16 2006 588 596
23. M. Rabani, J.Z. Levin, L. Fan, X. Adiconis, R. Raychowdhury, M. Garber, A. Gnirke, C. Nusbaum, N. Hacohen, N. Friedman, and et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells Nat. Biotechnol. 29 2011 436 442
24. V.R. Ramirez-Carrozzi, D. Braas, D.M. Bhatt, C.S. Cheng, C. Hong, K.R. Doty, J.C. Black, A. Hoffmann, M. Carey, and S.T. Smale A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling Cell 138 2009 114 128
25. S.A. Ramsey, S.L. Klemm, D.E. Zak, K.A. Kennedy, V. Thorsson, B. Li, M. Gilchrist, E.S. Gold, C.D. Johnson, V. Litvak, and et al. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics PLoS Comput. Biol. 4 2008 e1000021
26. M.D. Robinson, D.J. McCarthy, and G.K. Smyth edgeR: A Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics 26 2010 139 140
27. H.Y. Shih, G. Sciumè, A.C. Poholek, G. Vahedi, K. Hirahara, A.V. Villarino, M. Bonelli, R. Bosselut, Y. Kanno, S.A. Muljo, and J.J. O'Shea Transcriptional and epigenetic networks of helper T and innate lymphoid cells Immunol. Rev. 261 2014 23 49
28. T. Siggers, A.B. Chang, A. Teixeira, D. Wong, K.J. Williams, B. Ahmed, J. Ragoussis, I.A. Udalova, S.T. Smale, and M.L. Bulyk Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding Nat. Immunol. 13 2012 95 102
29. V. Toshchakov, B.W. Jones, P.-Y. Perera, K. Thomas, M.J. Cody, S. Zhang, B.R.G. Williams, J. Major, T.A. Hamilton, M.J. Fenton, and S.N. Vogel TLR4, but not TLR2, mediates IFN-beta-induced STAT1alpha/beta-dependent gene expression in macrophages Nat. Immunol. 3 2002 392 398
30. R. Treisman Ternary complex factors: Growth factor regulated transcriptional activators Curr. Opin. Genet. Dev. 4 1994 96 101
31. F. Zambelli, G. Pesole, and G. Pavesi Pscan: Finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes Nucleic Acids Res. 37 2009 W247 W252
32. B. Zhao, L.A. Barrera, I. Ersing, B. Willox, S.C.S. Schmidt, H. Greenfeld, H. Zhou, S.B. Mollo, T.T. Shi, K. Takasaki, and et al. The NF-κB genomic landscape in lymphoblastoid B cells Cell Rep. 8 2014 1595 1606