A genomic view of mRNA turnover in yeast

Comptes Rendus - Biologies

Volumn 334, Issue 8-9, 2011, Pages 647-654

  Pérez Ortín, José E ^a   Jordán Pla, Antonio ^a   Pelechano, Vicent ^b  

^a UNIVERSITY OF VALENCIA   (Spain)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

ChIP chip; Gene expression kinetics; mRNA stability; Run on; Transcription rate

Indexed keywords

MESSENGER RNA; RNA POLYMERASE;

DATA SET; DEGRADATION; EUKARYOTE; GENE EXPRESSION; GENOME; GENOMICS; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; RNA; TURNOVER; YEAST;

CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME; GENOMICS; KINETICS; NONHUMAN; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 79961170233     PISSN: 16310691     EISSN: 17683238     Source Type: Journal    
DOI: 10.1016/j.crvi.2011.05.013     Document Type: Article

References (52)

1. R. Parker, and H. Song The enzymes and control of eukaryotic mRNA turnover Nat. Struct. Mol. Biol. 11 2004 121 127 (Pubitemid 38146514)
2. J.E. Pérez-Ortín, J. García-Martínez, and T.M. Alberola DNA chips for yeast biotechnology. The case of wine yeasts J. Biotechnol. 98 2002 227 241 (Pubitemid 34874548)
3. J. García-Martínez, A. Aranda, and J.E. Pérez-Ortín Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms Mol. Cell. 15 2004 303 313 (Pubitemid 38950977)
4. V. Pelechano, and J.E. Pérez-Ortín There is a steady-state transcriptome in exponentially growing yeast cells Yeast 27 2010 413 422
5. D.L. Bentley, and M. Groudine A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells Nature 321 1986 702 706 (Pubitemid 16044131)
6. B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T.L. Volkert, C.J. Wilson, S.P. Bell, and R.A. Young Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309 (Pubitemid 32041573)
7. L.E. Rosaleny, A.B. Ruiz-García, J. García-Martínez, J.E. Pérez-Ortín, and V. Tordera The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes Genome. Biol. 8 2007 R119
8. P. Lefrancois, G.M. Euskirchen, R.K. Auerbach, J. Rozowsky, T. Gibson, C.M. Yellman, M. Gerstein, and M. Snyder Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing BMC Genomics 10 2009 37
9. H. Kim, B. Erickson, W. Luo, D. Seward, J.H. Graber, D.D. Pollock, P.C. Megee, and D.L. Bentley Gene-specific RNA polymerase II phosphorylation and the CTD code Nat. Struct. Mol. Biol. 17 2010 1279 1286
10. A. Mayer, M. Lidschreiber, M. Siebert, K. Leike, J. Soding, and P. Cramer Uniform transitions of the general RNA polymerase II transcription complex Nat. Struct. Mol. Biol. 17 2010 1272 1278
11. L.S. Churchman, and J.S. Weissman Nascent transcript sequencing visualizes transcription at nucleotide resolution Nature 469 2011 368 373
12. F. Carrillo Oesterreich, S. Preibisch, and K.M. Neugebauer Global analysis of nascent RNA reveals transcriptional pausing in terminal exons Mol. Cell. 40 2010 571 581
13. K. Hirayoshi, and J.T. Lis Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases Methods. Enzymol. 304 1999 351 362 (Pubitemid 29268892)
14. V. Pelechano, S. Chávez, and J.E. Pérez-Ortín A complete set of nascent transcription rates for yeast genes PLoS One 5 2010 e15442
15. M.M. Molina-Navarro, L. Castells-Roca, G. Bellí, J. García-Martínez, J. Marín-Navarro, J. Moreno, J.E. Pérez-Ortín, and E. Herrero Comprehensive transcriptional analysis of the oxidative response in yeast J. Biol. Chem. 283 2008 17908 17918
16. L. Romero-Santacreu, J. Moreno, J.E. Pérez-Ortín, and P. Alepuz Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae RNA 15 2009 1110 1120
17. L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
18. J. Fan, K. Zeller, Y.C. Chen, T. Watkins, K.C. Barnes, K.G. Becker, C.V. Dang, and C. Cheadle Time-dependent c-Myc transactomes mapped by Array-based nuclear run-on reveal transcriptional modules in human B cells PLoS One 5 2010 e9691
19. M. Ohtsu, M. Kawate, M. Fukuoka, W. Gunji, F. Hanaoka, T. Utsugi, F. Onoda, and Y. Murakami Novel DNA microarray system for analysis of nascent mRNAs DNA. Res. 15 2008 241 251
20. M.D. Cleary, C.D. Meiering, E. Jan, R. Guymon, and J.C. Boothroyd Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay Nat. Biotechnol. 23 2005 232 237 (Pubitemid 40255335)
21. M. Kenzelmann, S. Maertens, M. Hergenhahn, S. Kueffer, A. Hotz-Wagenblatt, L. Li, S. Wang, C. Ittrich, T. Lemberger, R. Arribas, S. Jonnakuty, M.C. Hollstein, W. Schmid, N. Gretz, H.J. Grone, and G. Schutz Microarray analysis of newly synthesized RNA in cells and animals Proc. Natl. Acad. Sci. U S A. 104 2007 6164 6169 (Pubitemid 47186066)
22. F.C. Holstege, E.G. Jennings, J.J. Wyrick, T.I. Lee, C.J. Hengartner, M.R. Green, T.R. Golub, E.S. Lander, and R.A. Young Dissecting the regulatory circuitry of a eukaryotic genome Cell 95 1998 717 728 (Pubitemid 28544132)
23. F. Robert, D.K. Pokholok, N.M. Hannett, N.J. Rinaldi, M. Chandy, A. Rolfe, J.L. Workman, D.K. Gifford, and R.A. Young Global position and recruitment of HATs and HDACs in the yeast genome Mol. Cell. 16 2004 199 209 (Pubitemid 39388835)
24. D.K. Pokholok, C.T. Harbison, S. Levine, M. Cole, N.M. Hannett, T.I. Lee, G.W. Bell, K. Walker, P.A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D.K. Gifford, and R.A. Young Genome-wide map of nucleosome acetylation and methylation in yeast Cell 122 2005 517 527 (Pubitemid 41191151)
25. Z. Xu, W. Wei, J. Gagneur, F. Perocchi, S. Clauder-Munster, J. Camblong, E. Guffanti, F. Stutz, W. Huber, and L.M. Steinmetz Bidirectional promoters generate pervasive transcription in yeast Nature 457 2009 1033 1037
26. J. Berretta, and A. Morillon Pervasive transcription constitutes a new level of eukaryotic genome regulation EMBO. Rep. 10 2009 973 982
27. R. Parker, D. Herrick, S.W. Peltz, and A. Jacobson Measurement of mRNA decay rates in Saccharomyces cerevisiae Methods. Enzymol. 194 1991 415 423
28. P. Sunnerhagen Cytoplasmatic post-transcriptional regulation and intracellular signalling Mol. Genet. Genomics. 277 2007 341 355 (Pubitemid 46452272)
29. Y. Wang, C.L. Liu, J.D. Storey, R.J. Tibshirani, D. Herschlag, and P.O. Brown Precision and functional specificity in mRNA decay Proc. Natl. Acad. Sci. U S A. 99 2002 5860 5865 (Pubitemid 34493230)
30. J. Grigull, S. Mnaimneh, J. Pootoolal, M.D. Robinson, and T.R. Hughes Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors Mol. Cell. Biol. 24 2004 5534 5547 (Pubitemid 38738184)
31. C.C. Friedel, and L. Dolken Metabolic tagging and purification of nascent RNA: implications for transcriptomics Mol. Biosyst. 5 2009 1271 1278
32. C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Dumcke, B. Zacher, A. Mayer, J. Sydow, L. Marcinowski, L. Dolken, D.E. Martin, A. Tresch, and P. Cramer Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast Mol. Syst. Biol. 7 2011 458
33. J.E. Pérez-Ortín, P.M. Alepuz, and J. Moreno Genomics and gene transcription kinetics in yeast Trends. Genet. 23 2007 250 257 (Pubitemid 46616969)
34. L. Castells-Roca, J. García-Martínez, J. Moreno, E. Herrero, G. Bellí, and J.E. Pérez-Ortín Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities PLoS One 6 2011 e17272
35. T.S. Kim, C.L. Liu, M. Yassour, J. Holik, N. Friedman, S. Buratowski, and O.J. Rando RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Genome. Biol. 11 2010 R75
36. M. Yassour, J. Pfiffner, J.Z. Levin, X. Adiconis, A. Gnirke, C. Nusbaum, D.A. Thompson, N. Friedman, and A. Regev Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Genome. Biol. 11 2010 R87
37. D. Zenklusen, D.R. Larson, and R.H. Singer Single-RNA counting reveals alternative modes of gene expression in yeast Nat. Struct. Mol. Biol. 15 2008 1263 1271
38. L.M. Hereford, and M. Rosbash Number and distribution of polyadenylated RNA sequences in yeast Cell 10 1977 453 462 (Pubitemid 8081711)
39. M. Bon, S.J. McGowan, and P.R. Cook Many expressed genes in bacteria and yeast are transcribed only once per cell cycle FASEB. J. 20 2006 1721 1723
40. G. Jona, M. Choder, and O. Gileadi Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast Biochim. Biophys. Acta. 1491 2000 37 48 (Pubitemid 30173331)
41. O. Shalem, O. Dahan, M. Levo, M.R. Martínez, I. Furman, E. Segal, and Y. Pilpel Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation Mol. Syst. Biol. 4 2008 223
42. B. Hayles, S. Yellaboina, and D. Wang Comparing transcription rate and mRNA abundance as parameters for biochemical pathway and network analysis PLoS One 5 2010 e9908
43. D.J. Hogan, D.P. Riordan, A.P. Gerber, D. Herschlag, and P.O. Brown Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system PLoS Biol 6 2008 e255
44. J.D Keene RNA regulons: coordination of post-transcriptional events Nat. Rev. Genet. 8 2007 533 543 (Pubitemid 46955210)
45. J. García-Martínez, F. González-Candelas, and J.E. Pérez-Ortín Common gene expression strategies revealed by genome-wide analysis in yeast Genome. Biol. 8 2007 R222
46. J. Fan, X. Yang, W. Wang, W.H. Wood 3rd., K.G. Becker, and M. Gorospe Global analysis of stress-regulated mRNA turnover by using cDNA arrays Proc. Natl. Acad. Sci. U S A. 99 2002 10611 10616
47. M. Schuhmacher, F. Kohlhuber, M. Holzel, C. Kaiser, H. Burtscher, M. Jarsch, G.W. Bornkamm, G. Laux, A. Polack, U.H. Weidle, and D. Eick The transcriptional program of a human B cell line in response to Myc Nucleic. Acids. Res. 29 2001 397 406 (Pubitemid 32060926)
48. M. Meininghaus, R.D. Chapman, M. Horndasch, and D. Eick Conditional expression of RNA polymerase II in mammalian cells. Deletion of the carboxyl-terminal domain of the large subunit affects early steps in transcription J. Biol. Chem. 275 2000 24375 24382 (Pubitemid 30626527)
49. C. Cheadle, J. Fan, Y.S. Cho-Chung, T. Werner, J. Ray, L. Do, M. Gorospe, and K.G. Becker Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability BMC. Genomics. 6 2005 75
50. S.A. Tenenbaum, C.C. Carson, U. Atasoy, and J.D. Keene Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera Gene 317 2003 79 87 (Pubitemid 37356920)
51. E.J. Steinmetz, C.L. Warren, J.N. Kuehner, B. Panbehi, A.Z. Ansari, and D.A. Brow Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase Mol. Cell. 24 2006 735 746 (Pubitemid 44839212)
52. V. Pelechano, and J.E. Pérez-Ortín The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast Yeast 25 2008 85 92 (Pubitemid 351279438)