A pre-initiation complex at the 3′-end of genes drives antisense transcription independent of divergent sense transcription

Nucleic Acids Research

Volumn 40, Issue 6, 2012, Pages 2432-2444

  Murray, Struan C ^a   Serra Barros, Ana ^a   Brown, David A ^a   Dudek, Peter ^a   Ayling, Jonathan ^a   Mellor, Jane ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE TRANSCRIPTION; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA FLANKING REGION; DNA STRUCTURE; GENE INSERTION; GENETIC TRANSCRIPTION; NONHUMAN; PRE INITIATION COMPLEX; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION;

3' FLANKING REGION; 5' FLANKING REGION; GALACTOKINASE; GENE EXPRESSION REGULATION, FUNGAL; PROMOTER REGIONS, GENETIC; RNA, ANTISENSE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TATA-BOX BINDING PROTEIN; TERMINATOR REGIONS, GENETIC; TRANS-ACTIVATORS; TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION, GENETIC;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84859335229     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1121     Document Type: Article

References (39)

1. Kapranov, P., Willingham, A.T. and Gingeras, T.R. (2007) Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet., 8, 413-423 (Pubitemid 46789245)
2. Berretta, J. and Morillon, A. (2009) Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep., 10, 973-982
3. Hongay, C.F., Grisafi, P.L., Galitski, T. and Fink, G.R. (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell, 127, 735-745 (Pubitemid 44716254)
4. Perocchi, F., Xu, Z., Clauder-Münster, S. and Steinmetz, L.M. (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res., 35, e128
5. Camblong, J., Iglesias, N., Fickentscher, F., Dieppois, G. and Stutz, F. (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell, 131, 706-717 (Pubitemid 350087198)
6. Nishizawa, M., Komai, T., Katou, Y., Shirahige, K., Ito, T. and Toh-e, A. (2008) Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast. PloS Biol., 6, 2817-2830
7. Pinskaya, M., Gourvennec, S. and Morillon, A. (2009) H3 lysine 4 di-and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J., 28, 1697-1707
8. Xu, Z., Wei, W., Gagneur, J., Clauder-Münster, S., Smolik, M., Huber, W. and Steinmetz, L.M. (2011) Antisense expression increases gene expression variability and locus interdependency. Mol. Syst. Biol., 7, 468
9. Mavrich, T.N., Ioshikhes, I.P., Venters, B.J., Jiang, C., Tomsho, L.P., Qi, J., Schuster, S.C., Albert, I. and Pugh, B.F. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res., 18, 1073-1083 (Pubitemid 351931158)
10. Venters, B.J. and Pugh, B.F. (2009) A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res., 19, 360-371
11. Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A.J., Tillo, D., Field, Y., LeProust, E.M., Hughes, T.R., Lieb, J.D., Widom, J. et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362-366
12. Chung, H.R., Dunkel, I., Heise, F., Linke, C., Krobitsch, S., Ehrenhofer-Murray, A.E., Sperling, S.R. and Vingron, M. (2010) The effect of micrococcal nuclease digestion on nucleosome positioning data. PloS ONE, 5, e15754
13. Neil, H., Malabat, C., d'Aubenton-Carafa, Y., Xu, Z., Steinmetz, L.M. and Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature, 457, 1038-1042
14. Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.C., Dufour, M.E., Boulay, J., Régnault, B., Devaux, F., Namane, A., Séraphin, B. et al. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell, 121, 725-737 (Pubitemid 40797595)
15. Churchman, L.S. and Weissman, J.S. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469, 368-373
16. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349 (Pubitemid 351929471)
17. Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. and Steinmetz, L.M. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature, 457, 1033-1037
18. Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A. et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl Acad. Sci. USA, 106, 3264-3269
19. Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. and Steinmetz, L.M. (2010) High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol., 11, R24
20. Yassour, M., Pfiffner, J., Levin, J.Z., Adiconis, X., Gnirke, A., Nusbaum, C., Thompson, D.A., Friedman, N. and Regev, A. (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol., 11, R87
21. Fan, X., Moqtaderi, Z., Jin, Y., Zhang, Y., Liu, X.S. and Struhl, K. (2010) Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc. Natl Acad. Sci. USA, 107, 17945-17950
22. MacIsaac, K.D., Wang, T., Gordon, D.B., Gifford, D.K., Stormo, G.D. and Fraenkel, E. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinform., 7, 113
23. Wach, A., Brachat, A., Pohlmann, R. and Philippsen, P. (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast, 10, 1793-1808
24. Longtine, M.S., McKenzie, A., Demarini, D.J., Shah, N.G., Wach, A., Brachat, A., Philippsen, P. and Pringle, J.R. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast, 14, 953-961 (Pubitemid 28328001)
25. Houseley, J., Rubbi, L., Grunstein, M., Tollervey, D. and Vogelauer, M. (2008) A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol. Cell, 32, 685-695
26. Güldener, U., Heck, S., Fielder, T., Beinhauer, J. and Hegemann, J.H. (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res., 24, 2519-2524 (Pubitemid 26237149)
27. Mizuguchi, G., Shen, X., Landry, J., Wu, W., Sen, S. and Wu, C. (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science, 303, 343-348 (Pubitemid 38095768)
28. Cairns, B.R., Lorch, Y., Li, Y., Zhang, M., Lacomis, L., Erdjument-Bromage, H., Tempst, P., Du, J., Laurent, B. and Kornberg, R.D. (1996) RSC, an essential, abundant chromatin-remodeling complex. Cell, 87, 1249-1260 (Pubitemid 27010108)
29. O'Sullivan, J.M., Tan-Wong, S.M.M., Morillon, A., Lee, B., Coles, J., Mellor, J. and Proudfoot, N.J. (2004) Gene loops juxtapose promoters and terminators in yeast. Nature Genet., 36, 1014-1018 (Pubitemid 39167501)
30. Singh, B.N.N. and Hampsey, M. (2007) A transcriptionindependent role for TFIIB in gene looping. Mol. Cell, 27, 806-816 (Pubitemid 47333227)
31. Medler, S., Al Husini, N., Raghunayakula, S., Mukundan, B., Aldea, A. and Ansari, A. (2011) Evidence for a complex of transcription factor IIB with poly(A) polymerase and cleavage factor 1 subunits required for gene looping. J. Biol. Chem., 286, 33709-33718
32. Bernstein, B.E., Liu, C.L.L., Humphrey, E.L., Perlstein, E.O. and Schreiber, S.L. (2004) Global nucleosome occupancy in yeast. Genome. Biol., 5, R62
33. Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. and Lieb, J.D. (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genet., 36, 900-905 (Pubitemid 39014111)
34. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., MacIsaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J., Reynolds, D.B., Yoo, J. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104 (Pubitemid 39215116)
35. van Dijk, E.L., Chen, C.L., d'Aubenton-Carafa, Y., Gourvennec, S., Kwapisz, M., Roche, V., Bertrand, C., Silvain, M., Legoix-Ne, P., Loeillet, S. et al. (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature, 475, 114-117
36. Struhl, K. (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol., 14, 103-105
37. Berretta, J., Pinskaya, M. and Morillon, A. (2008) A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes. Dev., 22, 615-626 (Pubitemid 351342434)
38. Uhler, J.P., Hertel, C. and Svejstrup, J.Q. (2007) A role for noncoding transcription in activation of the yeast PHO5 gene. Proc. Natl Acad. Sci. USA, 104, 8011-8016 (Pubitemid 47185867)
39. Thoden, J.B. and Holden, H.M. (2005) The molecular architecture of galactose mutarotase/UDP-galactose 4-epimerase from Saccharomyces cerevisiae. J. Biol. Chem., 280, 21900-21907. (Pubitemid 40827841)