Super-enhancers delineate disease-associated regulatory nodes in T cells

Nature

Volumn 520, Issue 7548, 2015, Pages 558-562

  Vahedi, Golnaz ^a   Kanno, Yuka ^a   Furumoto, Yasuko ^a   Jiang, Kan ^a   Parker, Stephen C J ^b,e   Erdos, Michael R ^b   Davis, Sean R ^c   Roychoudhuri, Rahul ^c   Restifo, Nicholas P ^c   Gadina, Massimo ^a   Tang, Zhonghui ^d   Ruan, Yijun ^d   Collins, Francis S ^b   Sartorelli, Vittorio ^a   O'Shea, John J ^a  

^a NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d JACKSON LABORATORY   (United States)

^e UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE; CYTOKINE RECEPTOR; TOFACITINIB; TRANSCRIPTION FACTOR; BACH2 PROTEIN, MOUSE; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; HISTONE ACETYLTRANSFERASE PCAF; JANUS KINASE 3; P300-CBP-ASSOCIATED FACTOR; PIPERIDINE DERIVATIVE; PYRIMIDINE DERIVATIVE; PYRROLE DERIVATIVE; UNTRANSLATED RNA;

DISEASE INCIDENCE; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC DIFFERENTIATION; GERM CELL; IMMUNE RESPONSE;

ARTICLE; BACH2 GENE; CELL STRUCTURE; GENE; GENE REPRESSION; HUMAN; IMMUNOCOMPETENT CELL; LYMPHOCYTE DIFFERENTIATION; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; SUPER ENHANCER; T LYMPHOCYTE; ANIMAL; ANTAGONISTS AND INHIBITORS; C57BL MOUSE; CELL DIFFERENTIATION; CELL LINEAGE; ENHANCER REGION; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION; GENETIC TRANSCRIPTION; GENETICS; HELPER CELL; IMMUNOLOGY; METABOLISM; MOUSE; PATHOLOGY;

ANIMALS; ARTHRITIS, RHEUMATOID; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; CELL DIFFERENTIATION; CELL LINEAGE; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; JANUS KINASE 3; MICE; MICE, INBRED C57BL; P300-CBP TRANSCRIPTION FACTORS; PIPERIDINES; PYRIMIDINES; PYRROLES; RNA, UNTRANSLATED; T-LYMPHOCYTES, HELPER-INDUCER; TRANSCRIPTION, GENETIC;

EID: 84928560965     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14154     Document Type: Article

References (32)

1. Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014).
2. Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
3. Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320-334 (2013).
4. Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
5. Parker, S. C. et al. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc. Natl Acad. Sci. USA 110, 17921-17926 (2013).
6. Dowen, J. M. et al. Control of cell identity genes occurs in insulated neighborhoods in Mammalian chromosomes. Cell 159, 374-387 (2014).
7. Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376-381 (2014).
8. Rada-Iglesias, A. et al. Aunique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011).
9. Kieffer-Kwon, K. R. et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155, 1507-1520 (2013).
10. Mousavi, K. et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol. Cell 51, 606-617 (2013).
11. Hu, G. et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nature Immunol. 14, 1190-1198 (2013).
12. Ciofani, M. et al. A validated regulatory network for Th17 cell specification. Cell 151, 289-303 (2012).
13. Roychoudhuri, R. et al. BACH2 represses effector programs to stabilize Treg-mediated immune homeostasis. Nature 498, 506-510 (2013).
14. Wei, L. et al. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity 32, 840-851 (2010).
15. Vahedi, G. et al. STATs shape the active enhancer landscape of T cell populations. Cell 151, 981-993 (2012).
16. McAllister, K. et al. Identification of BACH2 and RAD51B as rheumatoid arthritis susceptibility loci in a meta-analysis of genome-wide data. Arthritis Rheum. 65, 3058-3062 (2013).
17. Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nature Genet. 42, 1118-1125 (2010).
18. Sawcer, S. et al. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 476, 214-219 (2011).
19. Ferreira, M. A. et al. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. Lancet 378, 1006-1014 (2011).
20. Cooper, J. D. et al. Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nature Genet. 40, 1399-1401 (2008).
21. Lovén, J. et al. Revisiting global gene expression analysis. Cell 151, 476-482 (2012).
22. Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119-124 (2012).
23. Beecham, A. H. et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nature Genet. 45, 1353-1360 (2013).
24. McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnol. 28, 495-501 (2010).
25. Ghisletti, S. et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32, 317-328 (2010).
26. Nakayamada, S. et al. Early Th1 cell differentiation is marked by a Tfh cell-like transition. Immunity 35, 919-931 (2011).
27. Wei, G. et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35, 299-311 (2011).
28. Hawkins, R. D. et al. Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity 38, 1271-1284 (2013).
29. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
30. Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952-1958 (2009).
31. Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).
32. Morris, A. P. et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nature Genet. 44, 981-990 (2012).