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.
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 abound.
van der Merwe
G K
GK
BC Wine Research Center, Faculty of Agricultural Sciences, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
van Vuuren
H J
HJ
Cooper
T G
TG
D000581:Amidohydrolases; D001665:Binding Sites / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D050980:GATA Transcription Factors; D015870:Gene Expression; D020869:Gene Expression Profiling; D005800:Genes, Fungal / Q000235:genetics; D005809:Genes, Regulator / Q000235:genetics; D016681:Genome, Fungal; D007438:Introns / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D016297:Mutagenesis, Site-Directed; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics* / Q000502:physiology; D012097:Repressor Proteins; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D012689:Sequence Homology, Nucleic Acid; D015534:Trans-Activators; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism
C082970:DAL82 protein, S cerevisiae; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; C096100:GAT1 protein, S cerevisiae; D050980:GATA Transcription Factors; C071664:GLN3 protein, S cerevisiae; D008565:Membrane Proteins; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D000581:Amidohydrolases; C492138:DAL1 protein, S cerevisiae