Genomics and gene transcription kinetics in yeast

Trends in Genetics

Volumn 23, Issue 5, 2007, Pages 250-257

  Pérez Ortín, José E ^a   Alepuz, Paula M ^a   Moreno, Joaquín ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA POLYMERASE;

DNA MICROARRAY; EUKARYOTE; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOMICS; KINETICS; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN STABILITY; PROTEIN SYNTHESIS; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST;

FORECASTING; GENE EXPRESSION; GENOMICS; KINETICS; MODELS, GENETIC; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 34247238676     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2007.03.006     Document Type: Review

References (43)

1. Edwards A.M., et al. Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J. Biol. Chem. 266 (1991) 71-75
2. O'Brien T., and Lis J.T. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol. Cell. Biol. 13 (1993) 3456-3463
3. Tennyson C.N., et al. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat. Genet. 9 (1995) 184-190
4. Darzacq X., et al. Dynamics of transcription and mRNA export. Curr. Opin. Cell Biol. 17 (2005) 332-339
5. Bubulya P.A., and Spector D.L. On the movements of nuclear components in living cells. Exp. Cell Res. 296 (2004) 4-11
6. Dujon B. The yeast genome project: what did we learn?. Trends Genet. 12 (1996) 263-270
7. Hargrove J.L., et al. The kinetics of mammalian gene expression. BioEssays 13 (1991) 667-674
8. Cole C.N., and Scarcelli J.J. Transport of messenger RNA from the nucleus to the cytoplasm. Curr. Opin. Cell Biol. 18 (2006) 299-306
9. Yagil G. Quantitative aspects of protein induction. Curr. Top. Cell. Regul. 9 (1975) 183-236
10. García-Martínez J., et al. Genomic run-on evaluates transcription rates for all yeast genes and identifies new gene regulatory mechanisms. Mol. Cell 15 (2004) 303-313
11. DeRisi J.L., et al. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 (1997) 680-686
12. Wang Y., et al. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 5860-5865
13. Grigull J., et al. 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
14. Foat B.C., et al. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 17675-17680
15. Mata J., et al. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem. Sci. 30 (2005) 506-514
16. Shalgi R., et al. A catalog of stability-associated sequence elements in 3′ UTRs of yeast mRNAs. Genome Biol. 6 (2005) R86 10.1186/gb-2005-6-10-r86 (genomebiology.com)
17. Yang E., et al. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res. 13 (2003) 1863-1872
18. Lee A., et al. Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiae. Mol. Cell 19 (2005) 39-51
19. Cosma M.P. Ordered recruitment: gene-specific mechanism of transcription activation. Mol. Cell 10 (2002) 227-236
20. Fan J., et al. Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 10611-10616
21. Velculescu V.E., et al. Serial analysis of gene expression. Science 270 (1995) 484-487
22. Schena M., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
23. Hereford L.M., and Rosbash M. Number and distribution of polyadenylated RNA sequences in yeast. Cell 10 (1977) 453-462
24. Beyer A., et al. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics 3 (2004) 1083-1092
25. Parker R., et al. Measurement of mRNA decay rates in Saccharomyces cerevisiae. Methods Enzymol. 194 (1991) 415-423
26. Enriquez-Harris P., et al. A pause site for RNA polymerase II is associated with termination of transcription. EMBO J. 10 (1991) 1833-1842
27. Hirayoshi K., and Lis J.T. Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases. Methods Enzymol. 304 (1999) 351-362
28. Meininghaus M., et al. 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
29. Schuhmacher M., et al. The transcriptional program of a human B cell line in response to myc. Nucleic Acids Res. 29 (2001) 397-406
30. Lilly J.W., et al. The Chlamydomonas reinhardtii organellar genomes respond transcriptionally and post-transcriptionally to abiotic stimuli. Plant Cell 14 (2002) 2681-2706
31. Cheadle C., et al. Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability. BMC Genomics 6 (2005) 75. www.biomedcentral.com/bmcgenomics 10.1186/1471-2164-6-75
32. Tenenbaum S.A., et al. Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317 (2003) 79-87
33. Keene J.D., and Tenenbaum S.A. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 9 (2002) 1161-1167
34. Iyer V., and Struhl K. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 5208-5212
35. Holstege F.C., et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95 (1998) 717-728
36. Even S., et al. Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures. Microbiology 149 (2003) 1935-1944
37. Redon E., et al. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J. Biol. Chem. 280 (2005) 36380-36385
38. Ter Kuile B.H., and Westerhoff H.V. Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500 (2001) 169-171
39. Tu B.P., et al. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310 (2005) 1152-1158
40. Osley M.A. The regulation of histone synthesis in the cell cycle. Annu. Rev. Biochem. 60 (1991) 827-861
41. Ghaemmaghami S., et al. Global analysis of protein expression in yeast. Nature 425 (2003) 737-741
42. Arava Y., et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 3889-3894
43. Belle A., et al. Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 13004-13009