Dealing with pervasive transcription

Molecular Cell

Volumn 52, Issue 4, 2013, Pages 473-484

  Jensen, TorbenHeick ^a   Jacquier, Alain ^b   Libri, Domenico ^c  

^a AARHUS UNIVERSITY   (Denmark)

^b INSTITUT PASTEUR   (France)

^c CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; EXORIBONUCLEASE; GENERAL TRANSCRIPTION FACTOR; HISTONE DEACETYLASE; HISTONE H4; POLYCOMB REPRESSIVE COMPLEX 2; RNA HELICASE; RNA POLYMERASE; RNA POLYMERASE II; SMALL NUCLEAR RIBONUCLEOPROTEIN; TRANSCRIPTOME; MESSENGER RNA; UNTRANSLATED RNA;

BINDING SITE; CELL DIFFERENTIATION; CELLS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONFORMATIONAL TRANSITION; CYTOPLASM; DEACETYLATION; DIPLOIDY; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; EXOSOME; FLUORESCENCE IN SITU HYBRIDIZATION; GAMETOGENESIS; GENE SILENCING; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMIC INSTABILITY; HAPLOIDY; HISTONE METHYLATION; HUMAN; LUNG ADENOCARCINOMA; MAMMAL CELL; MEIOSIS; METASTASIS; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOSOME; NUCLEOTIDE METABOLISM; POLYADENYLATION; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; REGULON; REVIEW; RNA DEGRADATION; RNA INTERFERENCE; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; SPOROGENESIS; STEADY STATE; TATA BOX; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION TERMINATION; WILD TYPE; ANIMAL; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; RNA PROCESSING; RNA STABILITY;

ANIMALS; GENE EXPRESSION REGULATION; GENOME, FUNGAL; HUMANS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, MESSENGER; RNA, UNTRANSLATED; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 84888187077     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.10.032     Document Type: Review

References (123)

1. Almada A.E., Wu X., Kriz A.J., Burge C.B., Sharp P.A. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 2013, 499:360-363.
2. Andersen P., Domanski M., Kristiansen M.S., Storvall H., Ntini E., Verheggen C., Schein A., Bunkenborg J., Poser I., Hallais M., et al. The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat. Struct. Mol. Biol. 2013, 10.1038/nsmb.2703.
3. Arigo J.T., Eyler D.E., Carroll K.L., Corden J.L. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol. Cell 2006, 23:841-851.
4. Arigo J.T., Carroll K.L., Ames J.M., Corden J.L. Regulation of yeast NRD1 expression by premature transcription termination. Mol. Cell 2006, 21:641-651.
5. Ashe M.P., Griffin P., James W., Proudfoot N.J. Poly(A) site selection in the HIV-1 provirus: inhibition of promoter-proximal polyadenylation by the downstream major splice donor site. Genes Dev. 1995, 9:3008-3025.
6. Ashe H.L., Monks J., Wijgerde M., Fraser P., Proudfoot N.J. Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev. 1997, 11:2494-2509.
7. Beaulieu Y.B., Kleinman C.L., Landry-Voyer A.-M., Majewski J., Bachand F. Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet. 2012, 8:e1003078.
8. Berretta J., Pinskaya M., Morillon A. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev. 2008, 22:615-626.
9. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigó R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. ENCODE Project Consortium, NISC Comparative Sequencing ProgramNISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing CenterBaylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing CenterWashington University Genome Sequencing Center, Broad InstituteBroad Institute, Children's Hospital Oakland Research InstituteChildren's Hospital Oakland Research Institute.
10. Brockdorff N. Noncoding RNA and Polycomb recruitment. RNA 2013, 19:429-442.
11. Bumgarner S.L., Dowell R.D., Grisafi P., Gifford D.K., Fink G.R. Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc. Natl. Acad. Sci. USA 2009, 106:18321-18326.
12. Bumgarner S.L., Neuert G., Voight B.F., Symbor-Nagrabska A., Grisafi P., van Oudenaarden A., Fink G.R. Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol. Cell 2012, 45:470-482.
13. Calo E., Wysocka J. Modification of enhancer chromatin: what, how, and why?. Mol. Cell 2013, 49:825-837.
14. Camblong J., Iglesias N., Fickentscher C., Dieppois G., Stutz F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S.cerevisiae. Cell 2007, 131:706-717.
15. Camblong J., Beyrouthy N., Guffanti E., Schlaepfer G., Steinmetz L.M., Stutz F. Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev. 2009, 23:1534-1545.
16. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563. FANTOM Consortium, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
17. Carrozza M.J., Li B., Florens L., Suganuma T., Swanson S.K., Lee K.K., Shia W.-J., Anderson S., Yates J., Washburn M.P., Workman J.L. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005, 123:581-592.
18. Carvalho S., Raposo A.C., Martins F.B., Grosso A.R., Sridhara S.C., Rino J., Carmo-Fonseca M., de Almeida S.F. Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic Acids Res. 2013, 41:2881-2893.
19. Carvunis A.-R., Rolland T., Wapinski I., Calderwood M.A., Yildirim M.A., Simonis N., Charloteaux B., Hidalgo C.A., Barbette J., Santhanam B., et al. Proto-genes and de novo gene birth. Nature 2012, 487:370-374.
20. Castelnuovo M., Rahman S., Guffanti E., Infantino V., Stutz F., Zenklusen D. Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat. Struct. Mol. Biol. 2013, 20:851-858.
21. Churchman L.S., Weissman J.S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011, 469:368-373.
22. Core L.J., Waterfall J.J., Lis J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322:1845-1848.
23. Creamer T.J., Darby M.M., Jamonnak N., Schaughency P., Hao H., Wheelan S.J., Corden J.L. Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet. 2011, 7:e1002329.
24. Davis C.A., Ares M. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 2006, 103:3262-3267.
25. Dean A. On a chromosome far, far away: LCRs and gene expression. Trends Genet. 2006, 22:38-45.
26. De Santa F., Barozzi I., Mietton F., Ghisletti S., Polletti S., Tusi B.K., Muller H., Ragoussis J., Wei C.-L., Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010, 8:e1000384.
27. Djebali S., Davis C.A., Merkel A., Dobin A., Lassmann T., Mortazavi A., Tanzer A., Lagarde J., Lin W., Schlesinger F., et al. Landscape of transcription in human cells. Nature 2012, 489:101-108.
28. Domazet-Loso T., Tautz D. An evolutionary analysis of orphan genes in Drosophila. Genome Res. 2003, 13:2213-2219.
29. Flynn R.A., Almada A.E., Zamudio J.R., Sharp P.A. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl. Acad. Sci. USA 2011, 108:10460-10465.
30. Gudipati R.K., Villa T., Boulay J., Libri D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nat. Struct. Mol. Biol. 2008, 15:786-794.
31. Gudipati R.K., Xu Z., Lebreton A., Séraphin B., Steinmetz L.M., Jacquier A., Libri D. Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol. Cell 2012, 48:409-421.
32. Gudipati R.K., Neil H., Feuerbach F., Malabat C., Jacquier A. The yeast RPL9B gene is regulated by modulation between two modes of transcription termination. EMBO J. 2012, 31:2427-2437.
33. Guttman M., Rinn J.L. Modular regulatory principles of large non-coding RNAs. Nature 2012, 482:339-346.
34. Guttman M., Donaghey J., Carey B.W., Garber M., Grenier J.K., Munson G., Young G., Lucas A.B., Ach R., Bruhn L., et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011, 477:295-300.
35. Hainer S.J., Pruneski J.A., Mitchell R.D., Monteverde R.M., Martens J.A. Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev. 2011, 25:29-40.
36. Hallais M., Pontvianne F., Andersen P.R., Clerici M., Lener D., Benbahouche N.E.H., Gostan T., Vandermoere F., Robert M.-C., Cusack S., et al. CBC-ARS2 stimulate 3'-end maturation of multiple RNA families and favor cap-proximal processing. Nat. Struct. Mol. Biol. 2013, 10.1038/nsmb.2720.
37. Hansen T.B., Jensen T.I., Clausen B.H., Bramsen J.B., Finsen B., Damgaard C.K., Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013, 495:384-388.
38. Hnisz D., Abraham B.J., Lee T.I., Lau A., Saint-André V., Sigova A.A., Hoke H.A., Young R.A. Super-enhancers in the control of cell identity and disease. Cell 2013, Published online October 8, 2013. 10.1016/j.cell.2013.09.053.
39. Hongay C.F., Grisafi P.L., Galitski T., Fink G.R. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006, 127:735-745.
40. Houalla R., Devaux F., Fatica A., Kufel J., Barrass D., Torchet C., Tollervey D. Microarray detection of novel nuclear RNA substrates for the exosome. Yeast 2006, 23:439-454.
41. Houseley J., Kotovic K., El Hage A., Tollervey D. Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J. 2007, 26:4996-5006.
42. Houseley J., Rubbi L., Grunstein M., Tollervey D., Vogelauer M. A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol. Cell 2008, 32:685-695.
43. Hu W., Alvarez-Dominguez J.R., Lodish H.F. Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep. 2012, 13:971-983.
44. Jacquier A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 2009, 10:833-844.
45. Kaida D., Berg M.G., Younis I., Kasim M., Singh L.N., Wan L., Dreyfuss G. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 2010, 468:664-668.
46. Kaikkonen M.U., Spann N.J., Heinz S., Romanoski C.E., Allison K.A., Stender J.D., Chun H.B., Tough D.F., Prinjha R.K., Benner C., Glass C.K. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 2013, 51:310-325.
47. Kaplan C.D., Laprade L., Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 2003, 301:1096-1099.
48. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermüller J., Hofacker I.L., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
49. Katayama S., Tomaru Y., Kasukawa T., Waki K., Nakanishi M., Nakamura M., Nishida H., Yap C.C., Suzuki M., Kawai J., et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309:1564-1566. RIKEN Genome Exploration Research Group, Genome Science Group (Genome Network Project Core Group)Genome Science Group (Genome Network Project Core Group), FANTOM ConsortiumFANTOM Consortium.
50. Keller C., Adaixo R., Stunnenberg R., Woolcock K.J., Hiller S., Bühler M. HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts. Mol. Cell 2012, 47:215-227.
51. Keller C., Kulasegaran-Shylini R., Shimada Y., Hotz H.-R., Bühler M. Noncoding RNAs prevent spreading of a repressive histone mark. Nat. Struct. Mol. Biol. 2013, 20:994-1000.
52. Kelley D., Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012, 13:R107.
53. Keogh M.-C., Kurdistani S.K., Morris S.A., Ahn S.H., Podolny V., Collins S.R., Schuldiner M., Chin K., Punna T., Thompson N.J., et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 2005, 123:593-605.
54. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., van Oudenaarden A., 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.
55. Kim T., Buratowski S. Dimethylation of H3K4 by Set1 recruits theSet3 histone deacetylase complex to 5' transcribed regions. Cell 2009, 137:259-272.
56. Kim K.Y., Levin D.E. Mpk1 MAPK association with the Paf1 complex blocks Sen1-mediated premature transcription termination. Cell 2011, 144:745-756.
57. Kim T.-K., Hemberg M., Gray J.M., Costa A.M., Bear D.M., Wu J., Harmin D.A., Laptewicz M., Barbara-Haley K., Kuersten S., et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010, 465:182-187.
58. Kim H., Erickson B., Luo W., Seward D., Graber J.H., Pollock D.D., Megee P.C., Bentley D.L. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat. Struct. Mol. Biol. 2011, 17:1279-1286.
59. Kim T., Xu Z., Clauder-Münster S., Steinmetz L.M., Buratowski S. Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell 2012, 150:1158-1169.
60. Kopcewicz K.A., O'Rourke T.W., Reines D. Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts. Mol. Cell. Biol. 2007, 27:2821-2829.
61. Kowalczyk M.S., Hughes J.R., Garrick D., Lynch M.D., Sharpe J.A., Sloane-Stanley J.A., McGowan S.J., De Gobbi M., Hosseini M., Vernimmen D., et al. Intragenic enhancers act as alternative promoters. Mol. Cell 2012, 45:447-458.
62. Kubicek K., Cerna H., Holub P., Pasulka J., Hrossova D., Loehr F., Hofr C., Vanacova S., Stefl R. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes Dev. 2012, 26:1891-1896.
63. Kuehner J.N., Brow D.A. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol. Cell 2008, 31:201-211.
64. Lai F., Orom U.A., Cesaroni M., Beringer M., Taatjes D.J., Blobel G.A., Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013, 494:497-501.
65. Lam M.T.Y., Cho H., Lesch H.P., Gosselin D., Heinz S., Tanaka-Oishi Y., Benner C., Kaikkonen M.U., Kim A.S., Kosaka M., et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 2013, 498:511-515.
66. Lardenois A., Liu Y., Walther T., Chalmel F., Evrard B., Granovskaia M., Chu A., Davis R.W., Steinmetz L.M., Primig M. Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc. Natl. Acad. Sci. USA 2011, 108:1058-1063.
67. Latos P.A., Pauler F.M., Koerner M.V., Şenergin H.B., Hudson Q.J., Stocsits R.R., Allhoff W., Stricker S.H., Klement R.M., Warczok K.E., et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012, 338:1469-1472.
68. Lee J.T. Epigenetic regulation by long noncoding RNAs. Science 2012, 338:1435-1439.
69. Lemay J.-F., D'Amours A., Lemieux C., Lackner D.H., St-Sauveur V.G., Bähler J., Bachand F. The nuclear poly(A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs. Mol. Cell 2010, 37:34-45.
70. Lemieux C., Marguerat S., Lafontaine J., Barbezier N., Bähler J., Bachand F. A Pre-mRNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein. Mol. Cell 2011, 44:108-119.
71. Li W., Notani D., Ma Q., Tanasa B., Nunez E., Chen A.Y., Merkurjev D., Zhang J., Ohgi K., Song X., et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 2013, 498:516-520.
72. Lubas M., Christensen M.S., Kristiansen M.S., Domanski M., Falkenby L.G., Lykke-Andersen S., Andersen J.S., Dziembowski A., Jensen T.H. Interaction profiling identifies the human nuclear exosome targeting complex. Mol. Cell 2011, 43:624-637.
73. Luke B., Panza A., Redon S., Iglesias N., Li Z., Lingner J. The Rat1p 5' to 3' exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol. Cell 2008, 32:465-477.
74. Marquardt S., Hazelbaker D.Z., Buratowski S. Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species. Transcription 2011, 2:145-154.
75. Martens J.A., Laprade L., Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004, 429:571-574.
76. Martens J.A., Wu P.Y., Winston F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev. 2005, 19:2695-2704.
77. Mayer A., Lidschreiber M., Siebert M., Leike K., Söding J., Cramer P. Uniform transitions of the general RNA polymerase II transcription complex. Nat. Struct. Mol. Biol. 2010, 17:1272-1278.
78. Melo C.A., Drost J., Wijchers P.J., van de Werken H., de Wit E., Oude Vrielink J.A.F., Elkon R., Melo S.A., Léveillé N., Kalluri R., et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 2013, 49:524-535.
79. Memczak S., Jens M., Elefsinioti A., Torti F., Krueger J., Rybak A., Maier L., Mackowiak S.D., Gregersen L.H., Munschauer M., et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495:333-338.
80. Mousavi K., Zare H., Dell'orso S., Grontved L., Gutierrez-Cruz G., Derfoul A., Hager G.L., Sartorelli V. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol. Cell 2013, 51:606-617.
81. Murray S.C., Serra Barros A., Brown D.A., Dudek P., Ayling J., Mellor J. A pre-initiation complex at the 3'-end of genes drives antisense transcription independent of divergent sense transcription. Nucleic Acids Res. 2012, 40:2432-2444.
82. Neil H., Malabat C., d'Aubenton-Carafa Y., Xu Z., Steinmetz L.M., Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009, 457:1038-1042.
83. Ntini E., Järvelin A.I., Bornholdt J., Chen Y., Boyd M., Jørgensen M., Andersson R., Hoof I., Schein A., Andersen P.R., et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 2013, 20:923-928.
84. Pinskaya M., Gourvennec S., Morillon A. H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J. 2009, 28:1697-1707.
85. Porrua O., Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat. Struct. Mol. Biol. 2013, 20:884-891.
86. Porrua O., Hobor F., Boulay J., Kubicek K., D'Aubenton-Carafa Y., Gudipati R.K., Stefl R., Libri D. Invivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination. EMBO J. 2012, 31:3935-3948.
87. Preker P., Nielsen J., Kammler S., Lykke-Andersen S., Christensen M.S., Mapendano C.K., Schierup M.H., Jensen T.H. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008, 322:1851-1854.
88. Rhee H.S., Pugh B.F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 2012, 483:295-301.
89. Rinn J.L., Chang H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81:145-166.
90. Sanyal A., Lajoie B.R., Jain G., Dekker J. The long-range interaction landscape of gene promoters. Nature 2012, 489:109-113.
91. Schmitz K.-M., Mayer C., Postepska A., Grummt I. Interaction ofnoncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev. 2010, 24:2264-2269.
92. Seila A.C., Calabrese J.M., Levine S.S., Yeo G.W., Rahl P.B., Flynn R.A., Young R.A., Sharp P.A. Divergent transcription from active promoters. Science 2008, 322:1849-1851.
93. Siepel A. Darwinian alchemy: human genes from noncoding DNA. Genome Res. 2009, 19:1693-1695.
94. Sigova A.A., Mullen A.C., Molinie B., Gupta S., Orlando D.A., Guenther M.G., Almada A.E., Lin C., Sharp P.A., Giallourakis C.C., Young R.A. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. USA 2013, 110:2876-2881.
95. Steinmetz E.J., Conrad N.K., Brow D.A., Corden J.L. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature 2001, 413:327-331.
96. Steinmetz E.J., Ng S.B., Cloute J.P., Brow D.A. cis- and trans-acting determinants of transcription termination by yeast RNA polymerase II. Mol. Cell. Biol. 2006, 26:2688-2696.
97. Steinmetz E.J., Warren C.L., Kuehner J.N., Panbehi B., Ansari A.Z., Brow D.A. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell 2006, 24:735-746.
98. Sun S., Del Rosario B.C., Szanto A., Ogawa Y., Jeon Y., Lee J.T. Jpx RNA activates Xist by evicting CTCF. Cell 2013, 153:1537-1551.
99. Taft R.J., Glazov E.A., Cloonan N., Simons C., Stephen S., Faulkner G.J., Lassmann T., Forrest A.R.R., Grimmond S.M., Schroder K., et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 2009, 41:572-578.
100. Tan-Wong S.M., Zaugg J.B., Camblong J., Xu Z., Zhang D.W., Mischo H.E., Ansari A.Z., Luscombe N.M., Steinmetz L.M., Proudfoot N.J. Gene loops enhance transcriptional directionality. Science 2012, 338:671-675.
101. Tautz D., Domazet-Lošo T. The evolutionary origin of orphan genes. Nat. Rev. Genet. 2011, 12:692-702.
102. Thiebaut M., Kisseleva-Romanova E., Rougemaille M., Boulay J., Libri D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol. Cell 2006, 23:853-864.
103. Thiebaut M., Colin J., Neil H., Jacquier A., Séraphin B., Lacroute F., Libri D. Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S.cerevisiae. Mol. Cell 2008, 31:671-682.
104. Tripathi V., Ellis J.D., Shen Z., Song D.Y., Pan Q., Watt A.T., Freier S.M., Bennett C.F., Sharma A., Bubulya P.A., et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39:925-938.
105. Tuck A.C., Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013, 154:996-1009.
106. Ulitsky I., Bartel D.P. lincRNAs: genomics, evolution, and mechanisms. Cell 2013, 154:26-46.
107. Valen E., Preker P., Andersen P.R., Zhao X., Chen Y., Ender C., Dueck A., Meister G., Sandelin A., Jensen T.H. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 2011, 18:1075-1082.
108. van Dijk E.L., Chen C.L., d'Aubenton-Carafa Y., Gourvennec S., Kwapisz M., Roche V., Bertrand C., Silvain M., Legoix-Né P., Loeillet S., et al. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 2011, 475:114-117.
109. van Werven F.J., Neuert G., Hendrick N., Lardenois A., Buratowski S., van Oudenaarden A., Primig M., Amon A. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 2012, 150:1170-1181.
110. Vasiljeva L., Buratowski S. Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. Mol. Cell 2006, 21:239-248.
111. Vasiljeva L., Kim M., Mutschler H., Buratowski S., Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat. Struct. Mol. Biol. 2008, 15:795-804.
112. Vasiljeva L., Kim M., Terzi N., Soares L.M., Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol. Cell 2008, 29:313-323.
113. Venters B.J., Pugh B.F. Genomic organization of human transcription initiation complexes. Nature 2013, 502:53-58.
114. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
115. Whitehouse I., Rando O.J., Delrow J., Tsukiyama T. Chromatin remodelling at promoters suppresses antisense transcription. Nature 2007, 450:1031-1035.
116. Wlotzka W., Kudla G., Granneman S., Tollervey D. The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J. 2011, 30:1790-1803.
117. Wyers F., Rougemaille M., Badis G., Rousselle J.C., Dufour M.E., Boulay J., Régnault B., Devaux F., Namane A., Séraphin B., et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005, 121:725-737.
118. Xie L., Pelz C., Wang W., Bashar A., Varlamova O., Shadle S., Impey S. KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription. EMBO J. 2011, 30:1473-1484.
119. Xu Z., Wei W., Gagneur J., Perocchi F., Clauder-Münster S., Camblong J., Guffanti E., Stutz F., Huber W., Steinmetz L.M. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009, 457:1033-1037.
120. Xu Z., Wei W., Gagneur J., Clauder-Münster S., Smolik M., Huber W., Steinmetz L.M. Antisense expression increases gene expression variability and locus interdependency. Mol. Syst. Biol. 2011, 7:468.
121. Yadon A.N., Van de Mark D., Basom R., Delrow J., Whitehouse I., Tsukiyama T. Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol. Cell. Biol. 2010, 30:5110-5122.
122. Zhang B., Arun G., Mao Y.S., Lazar Z., Hung G., Bhattacharjee G., Xiao X., Booth C.J., Wu J., Zhang C., Spector D.L. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2012, 2:111-123.
123. Zhao J., Ohsumi T.K., Kung J.T., Ogawa Y., Grau D.J., Sarma K., Song J.J., Kingston R.E., Borowsky M., Lee J.T. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 2010, 40:939-953.