Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae

A word of caution when correlating cis-acting sequences with genome-wide expression analyses

G. K. van der Merwe, H. J.J. van Vuuren, Terrance Cooper

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Correlating genome-wide expression profiles with sequence searches of promoter regions is being used as a technique to identify putative binding sites for transacting factors or to refine consensus sequences of those already known. To evaluate the limitations of such an approach in our studies of GATA-mediated transcription in Saccharomyces cerevisiae, we identified the relative contributions made to DAL1 and DAL4 expression by each of five Gln3p-, and/or Gat1p-, and three Dal82p-binding site homologous sequences situated in the 829-bp intergenic region separating these highly related, divergently transcribed genes. Our data suggest that although the correlation of repeated sequences or sequence homologies appearing within promoter regions with expression profiles obtained from genome-wide transcription analyses can provide useful starting points for analyses of cis-acting sites, significant limitations and possibilities for misinterpretation also bound.

Original languageEnglish (US)
Pages (from-to)156-165
Number of pages10
JournalCurrent Genetics
Volume39
Issue number3
DOIs
StatePublished - Jan 1 2001

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Sequence Homology
Genetic Promoter Regions
Saccharomyces cerevisiae
Binding Sites
Genome
Intergenic DNA
Consensus Sequence
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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title = "Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae: A word of caution when correlating cis-acting sequences with genome-wide expression analyses",
abstract = "Correlating genome-wide expression profiles with sequence searches of promoter regions is being used as a technique to identify putative binding sites for transacting factors or to refine consensus sequences of those already known. To evaluate the limitations of such an approach in our studies of GATA-mediated transcription in Saccharomyces cerevisiae, we identified the relative contributions made to DAL1 and DAL4 expression by each of five Gln3p-, and/or Gat1p-, and three Dal82p-binding site homologous sequences situated in the 829-bp intergenic region separating these highly related, divergently transcribed genes. Our data suggest that although the correlation of repeated sequences or sequence homologies appearing within promoter regions with expression profiles obtained from genome-wide transcription analyses can provide useful starting points for analyses of cis-acting sites, significant limitations and possibilities for misinterpretation also bound.",
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T2 - A word of caution when correlating cis-acting sequences with genome-wide expression analyses

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AU - van Vuuren, H. J.J.

AU - Cooper, Terrance

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AB - Correlating genome-wide expression profiles with sequence searches of promoter regions is being used as a technique to identify putative binding sites for transacting factors or to refine consensus sequences of those already known. To evaluate the limitations of such an approach in our studies of GATA-mediated transcription in Saccharomyces cerevisiae, we identified the relative contributions made to DAL1 and DAL4 expression by each of five Gln3p-, and/or Gat1p-, and three Dal82p-binding site homologous sequences situated in the 829-bp intergenic region separating these highly related, divergently transcribed genes. Our data suggest that although the correlation of repeated sequences or sequence homologies appearing within promoter regions with expression profiles obtained from genome-wide transcription analyses can provide useful starting points for analyses of cis-acting sites, significant limitations and possibilities for misinterpretation also bound.

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