Integrator mediates the biogenesis of enhancer RNAs

Nature

Volumn 525, Issue 7569, 2015, Pages 399-403

  Lai, Fan ^a   Gardini, Alessandro ^a   Zhang, Anda ^a   Shiekhattar, Ramin ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENHANCER RNA; RNA; RNA POLYMERASE II; UNCLASSIFIED DRUG; CHROMATIN; LONG UNTRANSLATED RNA; MULTIPROTEIN COMPLEX; NUCLEAR PROTEIN; PROTEIN SUBUNIT;

BIOCHEMISTRY; CATALYSIS; ENZYME ACTIVITY; GENE EXPRESSION; METAZOAN; RNA;

ARTICLE; CARBOXY TERMINAL SEQUENCE; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; BIOCATALYSIS; BIOSYNTHESIS; CHEMISTRY; CHROMATIN; DEFICIENCY; ENHANCER REGION; GENE EXPRESSION REGULATION; GENETICS; HELA CELL LINE; HUMAN; METABOLISM; PROMOTER REGION; PROTEIN SUBUNIT; RNA PROCESSING; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

METAZOA;

BIOCATALYSIS; CHROMATIN; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MULTIPROTEIN COMPLEXES; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN SUBUNITS; RNA POLYMERASE II; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, LONG NONCODING; TRANSCRIPTION INITIATION, GENETIC; TRANSCRIPTION TERMINATION, GENETIC;

EID: 84940419156     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14906     Document Type: Article

References (31)

1. Baillat, D. et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265-276 (2005).
2. Wang, K. C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
3. Ørom, U. A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46-58 (2010).
4. De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).
5. Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
6. Bhatt, D. M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279-290 (2012).
7. Lam, M. T. et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511-515 (2013).
8. Li, W. et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516-520 (2013).
9. Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-394 (2011).
10. Sigova, A. A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl Acad. Sci. USA 110, 2876-2881 (2013).
11. Hah, N. et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145, 622-634 (2011).
12. Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
13. Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320-334 (2013).
14. Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
15. Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
16. Melo, C. A. et al. eRNAsare required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49, 524-535 (2013).
17. Mousavi, K. et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol. Cell 51, 606-617 (2013).
18. Gardini, A. et al. Integrator regulates transcriptional initiation and pause release following activation. Mol. Cell 56, 128-139 (2014).
19. Yamamoto, J. et al. DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. Nat. Commun. 5, 4263 (2014).
20. Albrecht, T. R. & Wagner, E. J. snRNA 3′ end formation requires heterodimeric association of integrator subunits. Mol. Cell. Biol. 32, 1112-1123 (2012).
21. Koch, F. et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nature Struct. Mol. Biol. 18, 956-963 (2011).
22. Yang, L. et al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 500, 598-602 (2013).
23. Stadelmayer, B. et al. Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat. Commun. 5, 5531 (2014).
24. Skaar, J. R. et al. The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res. 25, 288-305 (2015).
25. Schaukowitch, K. et al. Enhancer RNA facilitates NELF release from immediate early genes. Mol. Cell 56, 29-42 (2014).
26. Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
27. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
28. Wang, L. G., Wang, S. Q. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184-2185 (2012).
29. Ye, T. et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011).
30. 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).
31. Lai, F. et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494, 497-501 (2013).