Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

Daryi Wang, Huang-Mo Sung, Tzi Yuan Wang, Chih Jen Huang, Peggy Yang, Tiffany Chang, Yang Chao Wang, Da Lun Tseng, Jen Pey Wu, Tso Ching Lee, Ming Che Shih, Wen Hsiung Li

研究成果: Article

32 引文 (Scopus)

摘要

Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis-and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.

原文English
頁(從 - 到)1161-1169
頁數9
期刊Genome Research
17
發行號8
DOIs
出版狀態Published - 2007 八月 9

指紋

Trans-Activators
Yeasts
Gene Expression
Genes
Coculture Techniques
Diploidy
Regulator Genes
Alleles
Polymerase Chain Reaction
Messenger RNA
Mutation

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

引用此文

Wang, Daryi ; Sung, Huang-Mo ; Wang, Tzi Yuan ; Huang, Chih Jen ; Yang, Peggy ; Chang, Tiffany ; Wang, Yang Chao ; Tseng, Da Lun ; Wu, Jen Pey ; Lee, Tso Ching ; Shih, Ming Che ; Li, Wen Hsiung. / Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. 於: Genome Research. 2007 ; 卷 17, 編號 8. 頁 1161-1169.
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title = "Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors",
abstract = "Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis-and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45{\%} (18/40) can be attributed to differences in trans-acting factors alone, 17.5{\%} (7/40) mainly to trans-variations, 20{\%} (8/40) to both cis- and trans-acting factors, 7.5{\%} (3/40) mainly to cis-variations, and 10{\%} (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.",
author = "Daryi Wang and Huang-Mo Sung and Wang, {Tzi Yuan} and Huang, {Chih Jen} and Peggy Yang and Tiffany Chang and Wang, {Yang Chao} and Tseng, {Da Lun} and Wu, {Jen Pey} and Lee, {Tso Ching} and Shih, {Ming Che} and Li, {Wen Hsiung}",
year = "2007",
month = "8",
day = "9",
doi = "10.1101/gr.6328907",
language = "English",
volume = "17",
pages = "1161--1169",
journal = "Genome Research",
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Wang, D, Sung, H-M, Wang, TY, Huang, CJ, Yang, P, Chang, T, Wang, YC, Tseng, DL, Wu, JP, Lee, TC, Shih, MC & Li, WH 2007, 'Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors', Genome Research, 卷 17, 編號 8, 頁 1161-1169. https://doi.org/10.1101/gr.6328907

Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. / Wang, Daryi; Sung, Huang-Mo; Wang, Tzi Yuan; Huang, Chih Jen; Yang, Peggy; Chang, Tiffany; Wang, Yang Chao; Tseng, Da Lun; Wu, Jen Pey; Lee, Tso Ching; Shih, Ming Che; Li, Wen Hsiung.

於: Genome Research, 卷 17, 編號 8, 09.08.2007, p. 1161-1169.

研究成果: Article

TY - JOUR

T1 - Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

AU - Wang, Daryi

AU - Sung, Huang-Mo

AU - Wang, Tzi Yuan

AU - Huang, Chih Jen

AU - Yang, Peggy

AU - Chang, Tiffany

AU - Wang, Yang Chao

AU - Tseng, Da Lun

AU - Wu, Jen Pey

AU - Lee, Tso Ching

AU - Shih, Ming Che

AU - Li, Wen Hsiung

PY - 2007/8/9

Y1 - 2007/8/9

N2 - Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis-and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.

AB - Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis-and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.

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