Transcription control by long non-coding RNAs

Transcription

Volumn 3, Issue 2, 2012, Pages 78-86

  Faust, Tyler ^a   Frankel, Alan D ^a   D'Orso, Iván ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Chromatin; Epigenetic silencing; Large intergenic non coding RNAs; Long non coding RNAs; RNA polymerase ii; Transcription

Indexed keywords

7SK SMALL NUCLEAR RNA; ALU UNTRANSLATED RNA; B2 UNTRANSLATED RNA; COREPRESSOR PROTEIN; COREST PROTEIN; CYCLIN D1; HISTONE H3; OCTAMER TRANSCRIPTION FACTOR 4; POSITIVE TRANSCRIPTION ELONGATION FACTOR B; PROTEIN HOTAIR; RNA POLYMERASE II; RNA U1; SMALL NUCLEAR RNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

AIR GENE; ALU UNTRANSLATED RNA GENE; ARTICLE; B2 UNTRANSLATED RNA GENE; BINDING SITE; CHROMATIN STRUCTURE; CYCLIN D1 GENE; DHFR GENE; GENE; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LOCATION; GENE LOCUS; GENE SILENCING; HISTONE METHYLATION; HOTAIR GENE; HOXA TRANSCRIPT AT THE DISTAL TIP GENE; HUMAN; INSULATOR ELEMENT; KCNQ1OT1 GENE; MISTRAL GENE; NONHUMAN; OCT4 GENE; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA TRANSLATION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

EID: 84862741632     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.19349     Document Type: Article

References (97)

1. Morris KV, Santoso S, Turner AM, Pastori C, Hawkins PG. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 2008; 4:1000258. PMID:19008947; http://dx.doi.org/10.1371/journal.pgen.1000258.
2. Amaral PP, Dinger ME, Mercer TR, Mattick JS. The eukaryotic genome as an RNA machine. Science 2008; 319:1787-1789. PMID:18369136; http://dx.doi.org/10.1126/science.1155472.
3. Mattick JS, Taft RJ, Faulkner GJ. A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet 2010; 26:21-28. PMID:19944475; http://dx.doi.org/10.1016/j.tig.2009.11.002.
4. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, et al. The reality of pervasive transcription. PLoS Biol 2011; 9:1000625.
5. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, et al.; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium. Antisense transcription in the mammalian transcriptome. Science 2005; 309:1564-1566. PMID:16141073; http://dx.doi.org/10.1126/science.1112009.
6. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al.; ENCODE Project Consortium; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816. PMID:17571346; http://dx.doi.org/10.1038/nature05874.
7. van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most "dark matter" transcripts are associated with known genes. PLoS Biol 2010; 8:1000371. PMID:20502517; http://dx.doi.org/10.1371/journal.pbio.1000371.
8. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136:215-233. PMID:19167326; http://dx.doi.org/10.1016/j.cell.2009.01.002.
9. Jinek M, Doudna JA. A three-dimensional view of the molecular machinery of RNA interference. Nature 2009; 457:405-412. PMID:19158786; http://dx.doi.org/10.1038/nature07755.
10. Siomi MC, Sato K, Pezic D, Aravin AA. PIWIinteracting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 2011; 12:246-258. PMID:21427766; http://dx.doi.org/10.1038/nrm3089.
11. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-227. PMID:19182780; http://dx.doi.org/10.1038/nature07672.
12. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, et al. LincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477:295-300. PMID:21874018; http://dx.doi.org/10.1038/nature10398.
13. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol 2011; 21:354-361. PMID:21550244; http://dx.doi.org/10.1016/j.tcb.2011.04.001.
14. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25:1915-1927. PMID:21890647; http://dx.doi.org/10.1101/gad.17446611.
15. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, 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.
16. Kim TKHM, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-187. PMID:20393465; http://dx.doi.org/10.1038/nature09033.
17. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472:120-124. PMID:21423168; http://dx.doi.org/10.1038/nature09819.
18. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43:904-914. PMID:21925379; http://dx.doi.org/10.1016/j.molcel.2011.08.018.
19. Mellor J. Transcription: from regulatory ncRNA to incongruent redundancy. Genes Dev 2010; 24:1449-1455. PMID:20634311; http://dx.doi.org/10.1101/gad.1950310.
20. Lee JT. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb Perspect Biol 2010; 2:3749. PMID:20739414; http://dx.doi.org/10.1101/cshperspect.a003749.
21. Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell 2011; 145:178-181. PMID:21496640; http://dx.doi.org/10.1016/j.cell.2011.03.014.
22. Ørom UA, Shiekhattar R. Long non-coding RNAs and enhancers. Curr Opin Genet Dev 2011; 21:194-198. PMID:21330130; http://dx.doi.org/10.1016/j.gde.2011.01.020.
23. Clark MB, Mattick JS. Long noncoding RNAs in cell biology. Semin Cell Dev Biol 2011; 22:366-376. PMID:21256239; http://dx.doi.org/10.1016/j.semcdb.2011.01.001.
24. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823-837. PMID:17512414; http://dx.doi.org/10.1016/j.cell.2007.05.009.
25. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553-560. PMID:17603471; http://dx.doi.org/10.1038/nature06008.
26. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, et al. Divergent transcription from active promoters. Science 2008; 322:1849-1851. PMID:19056940; http://dx.doi.org/10.1126/science.1162253.
27. Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 2010; 7:249-257. PMID:20682450; http://dx.doi.org/10.1016/j.stem.2010.06.015.
28. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129:1311-1323. PMID:17604720; http://dx.doi.org/10.1016/j.cell.2007.05.022.
29. Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011; 469:343-349. PMID:21248841; http://dx.doi.org/10.1038/nature09784.
30. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 2011; 44:667-678. PMID:21963238; http://dx.doi.org/10.1016/j.molcel.2011.08.027.
31. Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol 2007; 9:1428-1435. PMID:18037880; http://dx.doi.org/10.1038/ncb1663.
32. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009; 106:11667-11672. PMID:19571010; http://dx.doi.org/10.1073/pnas.0904715106.
33. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329:689-693. PMID:20616235; http://dx.doi.org/10.1126/science.1192002.
34. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464:1071-1076. PMID:20393566; http://dx.doi.org/10.1038/nature08975.
35. Bertani S, Sauer S, Bolotin E, Sauer F. The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell 2011; 43:1040-1046. PMID:21925392; http://dx.doi.org/10.1016/j.molcel.2011.08.019.
36. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008; 454:126-130. PMID:18509338; http://dx.doi.org/10.1038/nature06992.
37. Seidl CI, Stricker SH, Barlow DP. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J 2006; 25:3565-3575. PMID:16874305; http://dx.doi.org/10.1038/sj.emboj.7601245.
38. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008; 322:1717-1720. PMID:18988810; http://dx.doi.org/10.1126/science.1163802.
39. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008; 32:232-246. PMID:18951091; http://dx.doi.org/10.1016/j.molcel.2008.08.022.
40. Hawkins PG, Morris KV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 2010; 1:165-175. PMID:21151833; http://dx.doi.org/10.4161/trns.1.3.13332.
41. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451:202-206. PMID:18185590; http://dx.doi.org/10.1038/nature06468.
42. Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP, Corey DR, et al. Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 2008; 15:842-848. PMID:18604220; http://dx.doi.org/10.1038/nsmb.1444.
43. Ren B. Transcription: Enhancers make non-coding RNA. Nature 2010; 465:173-174. PMID:20463730; http://dx.doi.org/10.1038/465173a.
44. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, et al. Extensive and coordinated transcription of noncoding RNAs within cell cycle promoters. Nat Genet 2011; 43:621-629. PMID:21642992; http://dx.doi.org/10.1038/ng.848.
45. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, et al. Histone modifications at human enhancers reflect global cell-typespecific gene expression. Nature 2009; 459:108-112. PMID:19295514; http://dx.doi.org/10.1038/nature07829.
46. Mattick JS. Linc-ing Long noncoding RNAs and enhancer function. Dev Cell 2010; 19:485-486. PMID:20951339; http://dx.doi.org/10.1016/j.devcel.2010.10.003.
47. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011; 43:630-638. PMID:21685913; http://dx.doi.org/10.1038/ng.857.
48. Espinoza CA, Ren B. Mapping higher order structure of chromatin domains. Nat Genet 2011; 43:615-616. PMID:21709679; http://dx.doi.org/10.1038/ng.869.
49. Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 2008; 451:796-801. PMID:18235444; http://dx.doi.org/10.1038/nature06634.
50. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007; 128:1231-1245. PMID:17382889; http://dx.doi.org/10.1016/j.cell.2006.12.048.
51. Yao H, Brick K, Evrard Y, Xiao T, Camerini-Otero RD, Felsenfeld G. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 2010; 24:2543-2555. PMID:20966046; http://dx.doi.org/10.1101/gad.1967810.
52. Colley SM, Leedman PJ. Steroid Receptor RNA Activator-A nuclear receptor coregulator with multiple partners: Insights and challenges. Biochimie 2011; 93:1966-1972. PMID:21807064; http://dx.doi.org/10.1016/j.biochi.2011.07.004.
53. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 1999; 97:17-27. PMID:10199399; http://dx.doi.org/10.1016/S0092-8674(00)80711-4.
54. Hatchell EC, Colley SM, Beveridge DJ, Epis MR, Stuart LM, Giles KM, et al. SLIRP, a small SRA binding protein, is a nuclear receptor corepressor. Mol Cell 2006; 22:657-668. PMID:16762838; http://dx.doi.org/10.1016/j.molcel.2006.05.024.
55. Sikorski TW, Buratowski S. The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol 2009; 21:344-351. PMID:19411170; http://dx.doi.org/10.1016/j.ceb.2009.03.006.
56. Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006; 41:105-178. PMID:16858867; http://dx.doi.org/10.1080/10409230600648736.
57. Blume SW, Meng Z, Shrestha K, Snyder RC, Emanuel PD. The 5'-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter. J Cell Biochem 2003; 88:165-180. PMID:12461786; http://dx.doi.org/10.1002/jcb.10326.
58. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007; 445:666-670. PMID:17237763; http://dx.doi.org/10.1038/nature05519.
59. Schmitz KM, Mayer C, Postepska A, Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 2010; 24:2264-2269. PMID:20952535; http://dx.doi.org/10.1101/gad.590910.
60. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008; 29:499-509. PMID:18313387; http://dx.doi.org/10.1016/j.molcel.2007.12.013.
61. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci USA 2009; 106:5569-5574. PMID:19307572; http://dx.doi.org/10.1073/pnas.0810738106.
62. Goodrich JA, Kugel JF. Dampening DNA binding: a common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biol 2010; 7:305-309. PMID:20436282; http://dx.doi.org/10.4161/rna.7.3.11910.
63. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004; 11:822-829. PMID:15300239; http://dx.doi.org/10.1038/nsmb812.
64. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription 2011; 2:45-49. PMID:21326911; http://dx.doi.org/1.4161/trns.2.1.14306.
65. Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 2007; 13:583-596. PMID:17307818; http://dx.doi.org/10.1261/rna.310307.
66. Kwek KY, Murphy S, Furger A, Thomas B, O'Gorman W, Kimura H, et al. U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat Struct Biol 2002; 9:800-805. PMID:12389039.
67. O'Gorman W, Thomas B, Kwek KY, Furger A, Akoulitchev A. Analysis of U1 small nuclear RNA interaction with cyclin H. J Biol Chem 2005; 280:36920-36925. PMID:16115885; http://dx.doi.org/10.1074/jbc.M505791200.
68. Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, et al. RNA polymerase is poised for activation across the genome. Nat Genet 2007; 39:1507-1511. PMID:17994021; http://dx.doi.org/10.1038/ng.2007.21.
69. Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 2007; 39:1512-1516. PMID:17994019; http://dx.doi.org/10.1038/ng.2007.26.
70. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007; 130:77-88. PMID:17632057; http://dx.doi.org/10.1016/j.cell.2007.05.042.
71. Saunders A, Core LJ, Lis JT. Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 2006; 7:557-567. PMID:16936696; http://dx.doi.org/10.1038/nrm1981.
72. Selth LA, Sigurdsson S, Svejstrup JQ. Transcript Elongation by RNA Polymerase II. Annu Rev Biochem 2010; 79:271-293. PMID:20367031; http://dx.doi.org/10.1146/annurev.biochem.78.062807.091425.
73. Marshall NF, Price DH. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J Biol Chem 1995; 270:12335-12338. PMID:7759473; http://dx.doi.org/10.1074/jbc.270.21.12335.
74. Peterlin BM, Price DH. Controlling the elongation phase of transcription with P-TEFb. Mol Cell 2006; 23:297-305. PMID:16885020; http://dx.doi.org/10.1016/j.molcel.2006.06.014.
75. Marshall NF, Peng J, Xie Z, Price DH. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J Biol Chem 1996; 271:27176-27183. PMID:8900211; http://dx.doi.org/10.1074/jbc.271.43.27176.
76. Nguyen VT, Kiss T, Michels AA, Bensaude O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001; 414:322-325. PMID:11713533; http://dx.doi.org/10.1038/35104581.
77. Yang Z, Zhu Q, Luo K, Zhou Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 2001; 414:317-322. PMID:11713532; http://dx.doi.org/10.1038/35104575.
78. Wassarman DA, Steitz JA. Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function. Mol Cell Biol 1991; 11:3432-3445. PMID:1646389.
79. Egloff S, Van Herreweghe E, Kiss T. Regulation of polymerase II transcription by 7SK snRNA: two distinct RNA elements direct P-TEFb and HEXIM1 binding. Mol Cell Biol 2006; 26:630-642. PMID:16382153; http://dx.doi.org/10.1128/MCB.26.2.630-642.2006.
80. Marz M, Donath A, Verstraete N, Nguyen VT, Stadler PF, Bensaude O. Evolution of 7SK RNA and its protein partners in metazoa. Mol Biol Evol 2009; 26:2821-2830. PMID:19734296; http://dx.doi.org/10.1093/molbev/msp198.
81. Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q. Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol Cell 2003; 12:971-982. PMID:14580347; http://dx.doi.org/10.1016/S1097-2765(03)00388-5.
82. Barboric M, Kohoutek J, Price JP, Blazek D, Price DH, Peterlin BM. Interplay between 7SK snRNA and oppositely charged regions in HEXIM1 direct the inhibition of P-TEFb. EMBO J 2005; 24:4291-4303. PMID:16362050; http://dx.doi.org/10.1038/sj.emboj.7600883.
83. Krueger BJ, Jeronimo C, Roy BB, Bouchard A, Barrandon C, Byers SA, et al. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res 2008; 36:2219-2229. PMID:18281698; http://dx.doi.org/10.1093/nar/gkn061.
84. Markert A, Grimm M, Martinez J, Wiesner J, Meyerhans A, Meyuhas O, et al. The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes. EMBO Rep 2008; 9:569-575. PMID:18483487; http://dx.doi.org/10.1038/embor.2008.72.
85. He N, Jahchan NS, Hong E, Li Q, Bayfield MA, Maraia RJ, et al. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol Cell 2008; 29:588-599. PMID:18249148; http://dx.doi.org/10.1016/j.molcel.2008.01.003.
86. Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, et al. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell 2007; 27:262-274. PMID:17643375; http://dx.doi.org/10.1016/j.molcel.2007.06.027.
87. Barboric M, Yik JH, Czudnochowski N, Yang Z, Chen R, Contreras X, et al. Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription. Nucleic Acids Res 2007; 35:2003-2012. PMID:17341462; http://dx.doi.org/10.1093/nar/gkm063.
88. Krueger BJ, Varzavand K, Cooper JJ, Price DH. The mechanism of release of P-TEFb and HEXIM1 from the 7SK snRNP by viral and cellular activators includes a conformational change in 7SK. PLoS One 2010; 5:12335. PMID:20808803; http://dx.doi.org/10.1371/journal.pone.0012335.
89. Muniz L, Egloff S, Ughy B, Jády BE, Kiss T. Controlling cellular P-TEFb activity by the HIV-1 transcriptional transactivator Tat. PLoS Pathog 2010; 6:1001152. PMID:20976203; http://dx.doi.org/10.1371/journal.ppat.1001152.
90. Sobhian B, Laguette N, Yatim A, Nakamura M, Levy Y, Kiernan R, et al. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol Cell 2010; 38:439-451. PMID:20471949; http://dx.doi.org/10.1016/j.molcel.2010.04.012.
91. D'Orso I, Frankel AD. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol 2010; 17:815-821. PMID:20562857; http://dx.doi.org/10.1038/nsmb.1827.
92. Hogg JR, Collins K. RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation. RNA 2007; 13:868-880. PMID:17456562; http://dx.doi.org/10.1261/rna.565207.
93. Michels AA, Nguyen VT, Fraldi A, Labas V, Edwards M, Bonnet F, et al. MAQ1 and 7SK RNA interact with CDK9/cyclin T complexes in a transcriptiondependent manner. Mol Cell Biol 2003; 23:4859-4869. PMID:12832472; http://dx.doi.org/10.1128/MCB.23.14.4859-4869.2003.
94. Barrandon C, Bonnet F, Nguyen VT, Labas V, Bensaude O. The transcription-dependent dissociation of P-TEFb-HEXIM1-7SK RNA relies upon formation of hnRNP-7SK RNA complexes. Mol Cell Biol 2007; 27:6996-7006. PMID:17709395; http://dx.doi.org/10.1128/MCB.00975-07.
95. Eilebrecht S, Brysbaert G, Wegert T, Urlaub H, Benecke BJ, Benecke A. 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation. Nucleic Acids Res 2011; 39:2057-2072. PMID:21087998; http://dx.doi.org/10.1093/nar/gkq1153.
96. Eilebrecht S, Bécavin C, Léger H, Benecke BJ, Benecke A. HMGA1-dependent and independent 7SK RNA gene regulatory activity. RNA Biol 2011; 8:143-157. PMID:21282977; http://dx.doi.org/10.4161/rna.8.1.14261.
97. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409-419. PMID:20673990; http://dx.doi.org/10.1016/j.cell.2010.06.040.