The role of Cis-Regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes

被引:18
作者
Leach, Lindsey J.
Zhang, Ze
Lu, Chenqi
Kearsey, Michael J.
Luo, Zewei [1 ]
机构
[1] Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England
[2] Fudan Univ, Inst Biostat, Lab Populat & Quantitat Genet, Shanghai 200433, Peoples R China
关键词
yeast; duplication; divergence; gene expression; cis motifs; genetic regulation;
D O I
10.1093/molbev/msm188
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Expression divergence of duplicate genes is widely believed to be important for their retention and evolution of new function, although the mechanism that determines their expression divergence remains unclear. We use a genetical genomics approach to explore divergence in genetical control of yeast duplicate genes created by a whole-genome duplication that occurred about 100 MYA and those with a younger duplication age. The analysis reveals that duplicate genes have a significantly higher probability of sharing common genetic control than pairs of singleton genes. The expression quantitative trait loci (eQTLs) have diverged completely for a high proportion of duplicate pairs, whereas a substantially larger proportion of duplicates share common regulatory motifs after 100 Myr of divergent evolution. The similarity in both genetical control and cis motif structure for a duplicate pair is a reflection of its evolutionary age. This study reveals that up to 20% of variation in expression between ancient duplicate gene pairs in the yeast genome can be explained by both cis motif divergence (similar to 8%) and by trans eQTL divergence (similar to 10%). Initially, divergence in all 3 aspects of cis motif structure, trans-genetical control, and expression evolves coordinately with the coding sequence divergence of both young and old duplicate pairs. These findings highlight the importance of divergence in both cis motif structure and trans-genetical control in the diverse set of mechanisms underlying the expression divergence of yeast duplicate genes.
引用
收藏
页码:2556 / 2565
页数:10
相关论文
共 52 条
[1]   Systematic management and analysis of yeast gene expression data [J].
Aach, J ;
Rindone, W ;
Church, GM .
GENOME RESEARCH, 2000, 10 (04) :431-445
[2]   BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments [J].
Al-Shahrour, F ;
Minguez, P ;
Vaquerizas, JM ;
Conde, L ;
Dopazo, J .
NUCLEIC ACIDS RESEARCH, 2005, 33 :W460-W464
[3]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[4]   CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].
BENJAMINI, Y ;
HOCHBERG, Y .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300
[5]   The landscape of genetic complexity across 5,700 gene expression traits in yeast [J].
Brem, RB ;
Kruglyak, L .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (05) :1572-1577
[6]   Genetic dissection of transcriptional regulation in budding yeast [J].
Brem, RB ;
Yvert, G ;
Clinton, R ;
Kruglyak, L .
SCIENCE, 2002, 296 (5568) :752-755
[7]   The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species [J].
Byrne, KP ;
Wolfe, KH .
GENOME RESEARCH, 2005, 15 (10) :1456-1461
[8]   Natural variation in human gene expression assessed in lymphoblastoid cells [J].
Cheung, VG ;
Conlin, LK ;
Weber, TM ;
Arcaro, M ;
Jen, KY ;
Morley, M ;
Spielman, RS .
NATURE GENETICS, 2003, 33 (03) :422-425
[9]   A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression [J].
Cohen, BA ;
Mitra, RD ;
Hughes, JD ;
Church, GM .
NATURE GENETICS, 2000, 26 (02) :183-186
[10]  
Conover W. J., 1980, PRACTICAL NONPARAMET