Roles of trans and cis variation in yeast intraspecies evolution of gene expression.
Both cis and trans mutations contribute to gene expression divergence within and between species. We used Saccharomyces cerevisiae as a model organism to estimate the relative contributions of cis and trans variations to the expression divergence between a laboratory (BY) and a wild (RM) strain of yeast. We examined whether genes regulated by a single transcription factor (TF; single input module, SIM genes) or genes regulated by multiple TFs (multiple input module, MIM genes) are more susceptible to trans variation. Because a SIM gene is regulated by a single immediate upstream TF, the chance for a change to occur in its trans-acting factors would, on average, be smaller than that for a MIM gene. We chose 232 genes that exhibited expression divergence between BY and RM to test this hypothesis. We examined the expression patterns of these genes in a BY-RM coculture system and in a BY-RM diploid hybrid. We found that trans variation is far more important than cis variation for expression divergence between the two strains. However, because in 75% of the genes studied, cis variation has significantly contributed to expression divergence, cis change also plays a significant role in intraspecific expression evolution. Interestingly, we found that the proportion of genes with diverged expression between BY and RM is larger for MIM genes than for SIM genes; in fact, the proportion tends to increase with the number of transcription factors that regulate the gene. Moreover, MIM genes are, on average, subject to stronger trans effects than SIM genes, though the difference between the two types of genes is not conspicuous.
Sung
Huang-Mo
HM
Genomics Research Center, Academia Sinica, Taipei, Taiwan.
Wang
Tzi-Yuan
TY
Wang
Daryi
D
Huang
Yu-Shan
YS
Wu
Jen-Pey
JP
Tsai
Huai-Kuang
HK
Tzeng
Jengnan
J
Huang
Chih-Jen
CJ
Lee
Yi-Chen
YC
Yang
Peggy
P
Hsu
Joyce
J
Chang
Tiffany
T
Cho
Chung-Yi
CY
Weng
Li-Chuan
LC
Lee
Tso-Ching
TC
Chang
Tien-Hsien
TH
Li
Wen-Hsiung
WH
Shih
Ming-Che
MC
D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D009154:Mutation / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA
D029701:Saccharomyces cerevisiae Proteins