Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

Molecular Systems Biology

Volumn 7, Issue , 2011, Pages

  Miller, Christian ^a   Schwalb, Björn ^a   Maier, Kerstin ^a   Schulz, Daniel ^a   Dümcke, Sebastian ^a   Zacher, Benedikt ^a   Mayer, Andreas ^a   Sydow, Jasmin ^a   Marcinowski, Lisa ^a   Dölken, Lars ^a   Martin, Dietmar E ^a   Tresch, Achim ^a   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA POLYMERASE II; SODIUM CHLORIDE; TRANSCRIPTION FACTOR; TRANSCRIPTOME; FUNGAL RNA;

ARTICLE; CELL CYCLE; CELL GROWTH; CONTROLLED STUDY; DYNAMIC TRANSCRIPTOME ANALYSIS; GENETIC TRANSCRIPTION; MESSENGER RNA SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA METABOLISM; STRESS; TRANSCRIPTOMICS; YEAST; BIOSYNTHESIS; DNA MICROARRAY; FUNGAL GENOME; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HALF LIFE TIME; METABOLISM; METHODOLOGY; PHYSIOLOGICAL STRESS; RNA STABILITY; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HALF-LIFE; LOGISTIC MODELS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA STABILITY; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 78650930357     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2010.112     Document Type: Article

References (59)

1. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, Florida: Chapman & Hall/CRC Press
2. Amorim MJ, Cotobal C, Duncan C, Mata J (2010) Global coordination of transcriptional control and mRNA decay during cellular differentiation. Mol Syst Biol 6: 380
3. Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC (2006) Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell 22: 179-192
4. Barreau C, Paillard L, Osborne HB (2005) AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res 33: 7138-7150
5. Brueckner F, Hennecke U, Carell T, Cramer P (2007) CPD damage recognition by transcribing RNA polymerase II. Science 315: 859-862
6. Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, OShea EK (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 40: 1300-1306
7. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA (2001) Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323-337
8. Cleary MD, Meiering CD, Jan E, Guymon R, Boothroyd JC (2005) Biosynthetic labeling of RNAwith uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat Biotechnol 23: 232-237
9. Courel M, Lallet S, Camadro JM, Blaiseau PL (2005) Direct activation of genes involved in intracellular iron use by the yeast ironresponsive transcription factor Aft2 without its paralog Aft1. Mol Cell Biol 25: 6760-6771
10. de Nadal E, Posas F (2010) Multilayered control of gene expression by stress-activated protein kinases. EMBO J 29: 4-13
11. Dengl S, Cramer P (2009) Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. J Biol Chem 284: 21270-21279
12. Dolken L, Ruzsics Z, Radle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, Koszinowski UH (2008) High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14: 1959-1972
13. Escote X, Zapater M, Clotet J, Posas F (2004) Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1. Nat Cell Biol 6: 997-1002
14. Friedel CC, Dolken L (2009) Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Mol BioSystems 5: 1271-1278
15. Garcia-Martinez J, Aranda A, Perez-Ortin JE (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 15: 303-313
16. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257
17. Gasch AP, Werner-Washburne M (2002) The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics 2: 181-192
18. Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24: 5534-5547
19. Halbeisen RE, Gerber AP (2009) Stress-Dependent Coordination of Transcriptome and Translatome in Yeast. PLoS Biol 7: e105
20. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104
21. Hereford LM, Rosbash M (1977) Number and distribution of polyadenylated RNA sequences in yeast. Cell 10: 453-462
22. Hinnebusch AG (2005) Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 59: 407-450
23. Hodson JA, Bailis JM, Forsburg SL (2003) Efficient labeling of fission yeast Schizosaccharomyces pombe with thymidine and BUdR. Nucleic Acids Res 31: e134
24. Hohmann S, Krantz M, Nordlander B (2007) Yeast osmoregulation. Methods Enzymol 428: 29-45
25. Holstege FC, Jennings EG,Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728
26. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31: 370-377
27. Kenzelmann M, Maertens S, Hergenhahn M, Kueffer S, Hotz- Wagenblatt A, Li L, Wang S, Ittrich C, Lemberger T, Arribas R, Jonnakuty S, Hollstein MC, SchmidW, Gretz N, Gröne HJ, Schütz G (2007) Microarray analysis of newly synthesized RNA in cells and animals. Proc Natl Acad Sci USA 104: 6164-6169
28. Lam LT, Pickeral OK, Peng AC, Rosenwald A, Hurt EM, Giltnane JM, Averett LM, Zhao H, Davis RE, Sathyamoorthy M,Wahl LM, Harris ED, Mikovits JA, Monks AP, Hollingshead MG, Sausville EA, Staudt LM (2001) Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. Genome Biol 2: RESEARCH0041
29. Macia J, Regot S, Peeters T, Conde N, Sole R, Posas F (2009) Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction. Sci Signal 2: ra13
30. MacIsaac KD,Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113
31. Mayer A, Lidschreiber M, Siebert M, Leike K, Söding J, Cramer P (2010) Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 10: 1272-1278
32. Melamed D, Pnueli L, Arava Y (2008) Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 14: 1337-1351
33. Melvin WT, Milne HB, Slater AA, Allen HJ, Keir HM (1978) Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur J Biochem 92: 373-379
34. Mettetal JT, Muzzey D, Gomez-Uribe C, van Oudenaarden A (2008) The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science 319: 482-484
35. Miller MR, Robinson KJ, Cleary MD, Doe CQ (2009) TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat Methods 6: 439-441
36. Molin C, Jauhiainen A,Warringer J, Nerman O, Sunnerhagen P (2009) mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress. RNA 15: 600-614
37. Muzzey D, Gomez-Uribe CA, Mettetal JT, van Oudenaarden A (2009) A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 138: 160-171
38. Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD (2006) A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124: 1069-1081
39. Park HY, Buxbaum AR, Singer RH (2010) Single mRNA tracking in live cells. Methods Enzymol 472: 387-406
40. Pelechano V, Jimeno-Gonzalez S, Rodriguez-Gil A, Garcia-Martinez J, Perez-Ortin JE, Chavez S (2009) Regulon-specific control of transcription elongation across the yeast genome. PLoS Genet 5: e1000614
41. Pelechano V, Perez-Ortin JE (2010) There is a steady-state transcriptome in exponentially growing yeast cells. Yeast 27: 413-422
42. Proft M, Struhl K (2004) MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction. Cell 118: 351-361
43. Rodriguez-Gil A, Garcia-Martinez J, Pelechano V, Munoz-Centeno MD, Geli V, Perez-Ortin JE, Chavez S (2010) The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res 38: 4651-4664
44. Romero-Santacreu L, Moreno J, Perez-Ortin JE, Alepuz P (2009) Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA 15: 1110-1120
45. Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 4: 223
46. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31: 265-273
47. Soufi B, Kelstrup CD, Stoehr G, Frohlich F,Walther TC, Olsen JV (2009) Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol Biosyst 5: 1337-1346
48. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539
49. Steinmetz EJ,Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA (2006) Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 24: 735-746
50. Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell 34: 710-721
51. Teixeira D, Parker R (2007) Analysis of P-body assembly in Saccharomyces cerevisiae. Mol Biol Cell 18: 2274-2287
52. Uesono Y, Toh EA (2002) Transient inhibition of translation initiation by osmotic stress. J Biol Chem 277: 13848-13855
53. Venters BJ, Pugh BF (2009) A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res 19: 360-371
54. Voth WP, Yu Y, Takahata S, Kretschmann KL, Lieb JD, Parker RL, Milash B, Stillman DJ (2007) Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J 26: 4324-4334
55. Vyas VK, Berkey CD, Miyao T, Carlson M (2005) Repressors Nrg1 and Nrg2 regulate a set of stress-responsive genes in Saccharomyces cerevisiae. Eukaryot Cell 4: 1882-1891
56. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99: 5860-5865
57. Warringer J, Hult M, Regot S, Posas F, Sunnerhagen P (2010) The HOG Pathway Dictates the Short-term Translational Response after Hyperosmotic Shock. Mol Biol Cell 21: 3080-3092
58. Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer FA (2004) A model based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 468: 909-917
59. Zacher B, Kuan P, Tresch A (2010) Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. BMC Bioinformatics 11: 194