Roles of trans and cis variation in yeast intraspecies evolution of gene expression

Huang Mo Sung, Tzi Yuan Wang, Daryi Wang, Yu Shan Huang, Jen Pey Wu, Huai Kuang Tsai, Jengnan Tzeng, Chih Jen Huang, Yi Chen Lee, Peggy Yang, Joyce Hsu, Tiffany Chang, Chung Yi Cho, Li Chuan Weng, Tso Ching Lee, Tien Hsien Chang, Wen Hsiung Li, Ming Che Shih

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28 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)2533-2538
Number of pages6
JournalMolecular Biology and Evolution
Issue number11
Publication statusPublished - 2009 Nov

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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