Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast.
In budding yeast, approximately a quarter of adjacent genes are divergently transcribed (divergent gene pairs). Whether genes in a divergent pair share the same regulatory system is still unknown. By examining transcription factor (TF) knockout experiments, we found that most TF knockout only altered the expression of one gene in a divergent pair. This prompted us to conduct a comprehensive analysis in silico to estimate how many divergent pairs are regulated by common sets of TFs (cis-regulatory modules, CRMs) using TF binding sites and expression data. Analyses of ten expression datasets show that only a limited number of divergent gene pairs share CRMs in any single dataset. However, around half of divergent pairs do share a regulatory system in at least one dataset. Our analysis suggests that genes in a divergent pair tend to be co-regulated in at least one condition; however, in most conditions, they may not be co-regulated.
Su
Chien-Hao
CH
Institute of Information Science, Academia Sinica, Taipei 115, Taiwan. d95922033@ntu.edu.tw
Shih
Ching-Hua
CH
Chang
Tien-Hsien
TH
Tsai
Huai-Kuang
HK
D001665:Binding Sites; D019295:Computational Biology; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors