title: Roles of trans and cis variation in yeast intraspecies evolution of gene expression.
abstract: 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.
authors: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors: Huang-Mo
authors: HM
authors: Sung
authors: Tzi-Yuan
authors: TY
authors: Wang
authors: Daryi
authors: D
authors: Wang
authors: Yu-Shan
authors: YS
authors: Huang
authors: Jen-Pey
authors: JP
authors: Wu
authors: Huai-Kuang
authors: HK
authors: Tsai
authors: Jengnan
authors: J
authors: Tzeng
authors: Chih-Jen
authors: CJ
authors: Huang
authors: Yi-Chen
authors: YC
authors: Lee
authors: Peggy
authors: P
authors: Yang
authors: Joyce
authors: J
authors: Hsu
authors: Tiffany
authors: T
authors: Chang
authors: Chung-Yi
authors: CY
authors: Cho
authors: Li-Chuan
authors: LC
authors: Weng
authors: Tso-Ching
authors: TC
authors: Lee
authors: Tien-Hsien
authors: TH
authors: Chang
authors: Wen-Hsiung
authors: WH
authors: Li
authors: Ming-Che
authors: MC
authors: Shih
mesh_terms: 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
chemical_list: D029701:Saccharomyces cerevisiae Proteins