IncRNA and gene looping: What's the connection?

Transcription

Volumn 5, Issue APR, 2014, Pages

  Shibayama, Youtaro ^a   Fanucchi, Stephanie ^a   Magagula, Loretta ^a   Mhlanga, Musa M ^a,b  

^a Biosciences Unit   (South Africa)

^b UNIVERSITY OF LISBON   (Portugal)

Author keywords

Chromatin contact; Chromatin loops; Enhancer; eRNA; Gene regulation; IncRNA; Multigene complex; Promoter; Topologically associating domain; Transcription

Indexed keywords

COHESIN; DNA; HEMOGLOBIN BETA CHAIN; RNA; TRANSCRIPTION FACTOR CTCF; CCCTC-BINDING FACTOR; CELL CYCLE PROTEIN; CHROMATIN; LONG UNTRANSLATED RNA; NONHISTONE PROTEIN; REPRESSOR PROTEIN;

ARTICLE; ENHANCER REGION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CLUSTER; GENE CONTROL; GENE DISRUPTION; GENE INTERACTION; GENE LOCUS; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENOME; HUMAN; NONHUMAN; PROMOTER REGION; PROTEIN DOMAIN; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; CHROMATIN; GENE EXPRESSION REGULATION; METABOLISM;

CELL CYCLE PROTEINS; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; REPRESSOR PROTEINS; RNA, LONG NONCODING; TRANSCRIPTION INITIATION, GENETIC;

EID: 84902374618     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.28658     Document Type: Article

References (31)

1. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002; 295:1306-11; PMID:11847345; http://dx.doi.org/10.1126/science.1067799
2. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326:289-93; PMID:19815776; http://dx.doi.org/10.1126/science.1181369
3. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012; 148:84-98; PMID:22265404; http://dx.doi.org/10.1016/j.cell.2011.12.014
4. Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung M-H, Li G, Resch W, Baek S, Pruett N, Grøntved L, et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2013; 155:1507-20; PMID:24360274; http://dx.doi.org/10.1016/j.cell.2013.11.039
5. Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233-44; PMID:22682246; http://dx.doi.org/10.1016/j.cell.2012.03.051
6. Fanucchi S, Shibayama Y, Burd S, Weinberg MS, Mhlanga MM. Chromosomal contact permits transcription between coregulated genes. Cell 2013; 155:606-20; PMID:24243018; http://dx.doi.org/10.1016/j.cell.2013.09.051
7. Cook PR. The organization of replication and transcription. Science 1999; 284:1790-5; PMID:10364545; http://dx.doi.org/10.1126/science.284.5421.1790
8. Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, et al. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012; 31:4404-14; PMID:23103767; http://dx.doi.org/10.1038/emboj.2012.288
9. Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, et al. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012; 2:1207-19; PMID:23103170; http://dx.doi.org/10.1016/j.celrep.2012.09.022
10. Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 2013; 341:664-7; PMID:23828889; http://dx.doi.org/10.1126/science.1239053
11. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet 2002; 32:623-6; PMID:12426570; http://dx.doi.org/10.1038/ng1051
12. Heintzman ND, Ren B. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev 2009; 19:541-9; PMID:19854636; http://dx.doi.org/10.1016/j.gde.2009.09.006
13. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143:46-58; PMID:20887892; http://dx.doi.org/10.1016/j.cell.2010.09.001
14. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013; 494:497-501; PMID:23417068; http://dx.doi.org/10.1038/nature11884
15. Kim T-K, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-7; PMID:20393465; http://dx.doi.org/10.1038/nature09033
16. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al.; FANTOM Consortium. An atlas of active enhancers across human cell types and tissues. Nature 2014; 507:455-61; PMID:24670763; http://dx.doi.org/10.1038/nature12787
17. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 2011; 474:390-4; PMID:21572438; http://dx.doi.org/10.1038/nature10006
18. Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 2011; 145:622-34; PMID:21549415; http://dx.doi.org/10.1016/j.cell.2011.03.042
19. Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R, et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 2013; 49:524-35; PMID:23273978; http://dx.doi.org/10.1016/j.molcel.2012.11.021
20. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 2013; 498:516-20; PMID:23728302; http://dx.doi.org/10.1038/nature12210
21. Lam MTY, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 2013; 498:511-5; PMID:23728303; http://dx.doi.org/10.1038/nature12209
22. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010; 467:430-5; PMID:20720539; http://dx.doi.org/10.1038/nature09380
23. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CWH, Ye C, Ping JLH, Mulawadi F, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011; 43:630-8; PMID:21685913; http://dx.doi.org/10.1038/ng.857
24. Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 2013; 153:1281-95; PMID:23706625; http://dx.doi.org/10.1016/j.cell.2013.04.053
25. Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J 2013; 32:3119-29; PMID:24185899; http://dx.doi.org/10.1038/emboj.2013.237
26. Zuin J, Dixon JR, van der Reijden MIJA, Ye Z, Kolovos P, Brouwer RWW, van de Corput MPC, van de Werken HJG, Knoch TA, van Ijcken WFJ, et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A 2014; 111:996-1001; PMID:24335803; http://dx.doi.org/10.1073/pnas.1317788111
27. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012; 485:376-80; PMID:22495300; http://dx.doi.org/10.1038/nature11082
28. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 2012; 148:458-72; PMID:22265598; http://dx.doi.org/10.1016/j.cell.2012.01.010
29. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012; 485:381-5; PMID:22495304; http://dx.doi.org/10.1038/nature11049
30. Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007; 29:288-99; PMID:17295292; http://dx.doi.org/10.1002/bies.20544
31. Yang L, Lin C, Jin C, Yang JC, Tanasa B, Li W, Merkurjev D, Ohgi KA, Meng D, Zhang J, et al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 2013; 500:598-602; PMID:23945587; http://dx.doi.org/10.1038/nature12451