Common gene expression strategies revealed by genome-wide analysis in yeast

Genome Biology

Volumn 8, Issue 10, 2007, Pages

  García Martínez, José ^a   González Candelas, Fernando ^b   Pérez Ortín, José E ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEASOME; PROTEIN SUBUNIT; MULTIPROTEIN COMPLEX;

ARTICLE; CELL GROWTH; CONTROLLED STUDY; CORRELATION ANALYSIS; FUNGAL CELL; FUNGAL GENE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENOME ANALYSIS; PROTEIN STABILITY; PROTEIN SYNTHESIS REGULATION; RIBOSOME; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION; TRANSLATION REGULATION; BIOLOGY; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; RNA STABILITY;

SACCHAROMYCES CEREVISIAE;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MULTIPROTEIN COMPLEXES; RNA STABILITY; SACCHAROMYCES CEREVISIAE;

EID: 42949122680     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-10-r222     Document Type: Article

References (40)

1. Crick FHC On protein synthesis. Symp Soc Exp Biol 1958 13 138-163
2. Pérez-Ortín JE Alepuz P Moreno J Genomics and the gene transcription kinetics in yeast. Trends Genet 2007 23 250-257 10.1016/ j.tig.2007.03.006 17379352
3. Fraser HB Hirsch AE Giaever G Kumm J Eisen M Noise minimization in eukaryotic gene expression. PLOS Biol 2004 2 e137 400249 15124029 10.1371/journal.pbio.0020137
4. Newman JRS Ghaemmaghami S Ihmels J Breslow DK Noble M Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006 441 840-846 10.1038/nature04785 16699522
5. Bar-Even A Paulsson J Maheshri N Carmi M O'Shea E Pilpel Y Barkai N Noise in protein expression scales with natural protein abundance. Nat Genet 2006 38 636-643 10.1038/ng1807 16715097
6. Warner JR Vilardell J Sohn JH Economics of ribosome biosynthesis. Cold Spring Harb Symp Quant Biol 2001 66 567-574 10.1101/sqb.2001.66.567 12762058
7. Mata J Marguerat S Bahler J Post-transcriptional control of gene expression: A genome-wide perspective. Trends Biochem Sci 2005 30 506-514 10.1016/j.tibs.2005.07.005 16054366
8. Greenbaum D Colangelo C Williams K Gerstein M Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003 4 117 193646 12952525 10.1186/gb-2003-4-9-117
9. Belle A Tanay A Bitincka L Shamir R O'Shea E Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA 2006 103 13004-13009 1550773 16916930 10.1073/pnas.0605420103
10. MacKay VL Li X Flory MR Turcott E Law GL Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics 2004 3 478-489 10.1074/mcp.M300129-MCP200 14766929
11. Lu P Vogel C Wang R Yao X Marcotte EM Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2007 25 117-124 10.1038/nbt1270 17187058
12. Pradet-Balade B Boulme F Beug H Mullner EW García-Sanz JA Translation control: Bridging the gap between genomics and proteomics? Trends Biochem Sci 2001 26 225-229 10.1016/S0968-0004(00)01776-X 11295554
13. Greenbaum D Jansen R Gerstein M Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 2002 18 585-596 10.1093/bioinformatics/18.4.585 12016056
14. Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000 11 4241-4257 15070 11102521
15. Lackner DH Beilharz TH Marguerat S Mata J Watt S Schubert F Preiss T Bahler J A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell 2007 26 145-55 1885965 17434133 10.1016/ j.molcel.2007.03.002
16. Velculescu VE Zhang L Zhou W Vogelstein J Basrai MA Bassett DE Jr Hieter P Vogelstein B Kinzler KW Characterization of the yeast transcriptome. Cell 1997 88 243-251 10.1016/S0092-8674(00)81845-0 9008165
17. Beyer A Hollunder J Nasheuer HP Wilhelm T Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 2004 3 1083-1092 10.1074/mcp.M400099-MCP200 15326222
18. Ghaemmaghami S Huh WK Bower K Howson RW Belle A Dephoure N O'Shea EK Weissman JS Global analysis of protein expression in yeast. Nature 2003 425 737-741 10.1038/nature02046 14562106
19. García-Martínez J Aranda A Pérez-Ortín JE Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 2004 15 303-313 10.1016/ j.molcel.2004.06.004 15260981
20. Arava Y Wang Y Storey JD Liu CL Brown PO Herschlag D Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003 100 3889-3894 153018 12660367 10.1073/ pnas.0635171100
21. Law GL Bickel KS MacKay VL Morris DR The undertranslated transcriptome reveals widespread translational silencing by alternative 5′ transcript leaders. Genome Biol 2005 6 R111 1414110 16420678 10.1186/ gb-2005-6-13-r111
22. Wang Y Liu CL Storey JD Tibshirani RJ Herschlag D Brown PO Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 2002 99 5860-5865 122867 11972065 10.1073/pnas.092538799
23. Grigull J Mnaimneh S Pootoolal J Robinson MD Hughes TR Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 2004 24 5534-5547 419893 15169913 10.1128/ MCB.24.12.5534-5547.2004
24. Yagil G Quantitative aspects of protein induction. Curr Top Cell Regul 1975 9 183-236 1091414
25. Herrero J Valencia A Dopazo J A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 2001 17 126-136 10.1093/bioinformatics/17.2.126 11238068
26. Vaquerizas JM Conde L Yankilevich P Cabezón A Mínguez P Díaz-Uriarte R Al-Shahrour F Herrero J Dopazo J GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 2005 33 Web Server W616-W620 1160260 15980548 10.1093/nar/gki500
27. Bader GD Heilbut A Andrews B Tyers M Hughes T Boone C Functional genomics and proteomics: Charting a multidimensional map of the yeast cell. Trends Cell Biol 2003 13 344-356 10.1016/S0962-8924(03)00127-2 12837605
28. Holland MJ Transcript abundance in yeast varies over six orders of magnitude. J Biol Chem 2002 277 14363-14366 10.1074/jbc.C200101200 11882647
29. Jansen R Gerstein M Analyzing protein function on a genomic scale: The importance of glod-standard positives and negatives for network prediction. Curr Opin Microbiol 2004 7 535-545 10.1016/j.mib.2004.08.012 15451510
30. Bernstein JA Khodursky AB Lin PH Lin-Chao S Cohen SN Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 2002 99 9697-9702 124983 12119387 10.1073/pnas.112318199
31. Andersson AF Lundgren M Eriksson S Rosenlund M Bernander R Nilsson P Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol 2006 7 R99 1794556 17067383 10.1186/gb-2006-7-10-r99
32. Gibbons FH Roth FP Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res 2002 12 1574-1581 187526 12368250 10.1101/gr.397002
33. Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions. Genome Res 2002 12 37-46 155252 11779829 10.1101/gr.205602
34. Deszo Z Oltvai ZN Barabási AL Bioinformatic analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res 2003 13 2450-2454 403764 14559778 10.1101/ gr.1073603
35. Tsay Y-F Thompson JR Rotemberg MO Larkin JC Woolford JL Ribosomal protein synthesis is not regulated at the translation level in Saccharomyces cerevisiae: Balanced accumulation of ribosomal proteins L16 and rp59 is mediated by turnover of excess protein. Genes Develop 1988 2 664-676 10.1101/gad.2.6.664 3047007
36. Bachand F Lackner DH Bahler J Silver PA Autoregulation of ribosome biosynthesis by a translational response in fission yeast. Mol Cell Biol 2006 26 1731-1742 1430238 16478994 10.1128/MCB.26.5.1731-1742.2006
37. Mnaimneh S Davierwala AP Haynes J Moffat J Peng WT Zhang W Yang X Pootoolal J Chua G Lopez A et al. Exploration of essential gene functions via titratable promoter alleles. Cell 2004 118 31-44 10.1016/ j.cell.2004.06.013 15242642
38. Hartigan JA Wong MA A K-means clustering algorithm. App Statist 1978 28 100-108 10.2307/2346830
39. Berriz GF King OD Bryant B Sander C Roth FP Characterizing gene sets with FuncAssociate. Bioinformatics 2003 19 2502-2504 10.1093/ bioinformatics/btg363 14668247
40. Staub E Mackowiak S Vingron M An inventory of yeast proteins associated with nucleolar and ribosomal components. Genome Biol 2006 7 R98 1794573 17067374 10.1186/gb-2006-7-10-r98