Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations

Alistair J.P. Brown, Rudi J. Planta, Fajar Restuhadi, David A. Bailey, Philip R. Butler, Jose L. Cadahia, M. Esperanza Cerdan, Martine De Jonge, David C.J. Gardner, Manda E. Gent, Andrew Hayes, Carin P.A.M. Kolen, Luis J. Lombardia, Abdul Munir Abdul Murad, Rachel A. Oliver, Mark Sefton, Johan M. Thevelein, Helene Tournu, Yvon J. Van Delft, Dennis J. VerbartJoris Winderickx, Stephen G. Oliver

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

The expression of 1008 open reading frames (ORFs) from the yeast Saccharomyces cerevisiae has been examined under eight different physiological conditions, using classical northern analysis. These northern data have been compared with publicly available data from a microarray analysis of the diauxic transition in S.cerevisiae. The results demonstrate the importance of comparing biologically equivalent situations and of the standardization of data normalization procedures. We have also used our northern data to identify co-regulated gene clusters and define the putative target sites of transcriptional activators responsible for their control. Clusters containing genes of known function identify target sites of known activators. In contrast, clusters comprised solely of genes of unknown function usually define novel putative target sites. Finally, we have examined possible global controls on gene expression. It was discovered that ORFs that are highly expressed following a nutritional upshift tend to employ favoured codons, whereas those overexpressed in starvation conditions do not. These results are interpreted in terms of a model in which competition between mRNA molecules for translational capacity selects for codons translated by abundant tRNAs.

Original languageEnglish (US)
Pages (from-to)3177-3186
Number of pages10
JournalEMBO Journal
Volume20
Issue number12
DOIs
StatePublished - Jun 15 2001

Fingerprint

Multigene Family
Codon
Yeast
Open Reading Frames
Saccharomyces cerevisiae
Genes
Yeasts
Throughput
Microarray Analysis
Starvation
Transfer RNA
Microarrays
Gene Expression
Gene expression
Standardization
Messenger RNA
Molecules

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Brown, A. J. P., Planta, R. J., Restuhadi, F., Bailey, D. A., Butler, P. R., Cadahia, J. L., ... Oliver, S. G. (2001). Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. EMBO Journal, 20(12), 3177-3186. https://doi.org/10.1093/emboj/20.12.3177

Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. / Brown, Alistair J.P.; Planta, Rudi J.; Restuhadi, Fajar; Bailey, David A.; Butler, Philip R.; Cadahia, Jose L.; Cerdan, M. Esperanza; De Jonge, Martine; Gardner, David C.J.; Gent, Manda E.; Hayes, Andrew; Kolen, Carin P.A.M.; Lombardia, Luis J.; Abdul Murad, Abdul Munir; Oliver, Rachel A.; Sefton, Mark; Thevelein, Johan M.; Tournu, Helene; Van Delft, Yvon J.; Verbart, Dennis J.; Winderickx, Joris; Oliver, Stephen G.

In: EMBO Journal, Vol. 20, No. 12, 15.06.2001, p. 3177-3186.

Research output: Contribution to journalArticle

Brown, AJP, Planta, RJ, Restuhadi, F, Bailey, DA, Butler, PR, Cadahia, JL, Cerdan, ME, De Jonge, M, Gardner, DCJ, Gent, ME, Hayes, A, Kolen, CPAM, Lombardia, LJ, Abdul Murad, AM, Oliver, RA, Sefton, M, Thevelein, JM, Tournu, H, Van Delft, YJ, Verbart, DJ, Winderickx, J & Oliver, SG 2001, 'Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations', EMBO Journal, vol. 20, no. 12, pp. 3177-3186. https://doi.org/10.1093/emboj/20.12.3177
Brown AJP, Planta RJ, Restuhadi F, Bailey DA, Butler PR, Cadahia JL et al. Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. EMBO Journal. 2001 Jun 15;20(12):3177-3186. https://doi.org/10.1093/emboj/20.12.3177
Brown, Alistair J.P. ; Planta, Rudi J. ; Restuhadi, Fajar ; Bailey, David A. ; Butler, Philip R. ; Cadahia, Jose L. ; Cerdan, M. Esperanza ; De Jonge, Martine ; Gardner, David C.J. ; Gent, Manda E. ; Hayes, Andrew ; Kolen, Carin P.A.M. ; Lombardia, Luis J. ; Abdul Murad, Abdul Munir ; Oliver, Rachel A. ; Sefton, Mark ; Thevelein, Johan M. ; Tournu, Helene ; Van Delft, Yvon J. ; Verbart, Dennis J. ; Winderickx, Joris ; Oliver, Stephen G. / Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. In: EMBO Journal. 2001 ; Vol. 20, No. 12. pp. 3177-3186.
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