Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape

Zou, Yangyun, Su, Zhixi, Yang, Jian, Zeng, Yanwu and Gu, Xun (2009) Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 312B 7: 722-733. doi:10.1002/jez.b.21290


Author Zou, Yangyun
Su, Zhixi
Yang, Jian
Zeng, Yanwu
Gu, Xun
Title Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape
Journal name Journal of Experimental Zoology Part B: Molecular and Developmental Evolution   Check publisher's open access policy
ISSN 1552-5007
1552-5015
Publication date 2009-11
Year available 2009
Sub-type Article (original research)
DOI 10.1002/jez.b.21290
Open Access Status
Volume 312B
Issue 7
Start page 722
End page 733
Total pages 12
Place of publication Hoboken, United States
Publisher John Wiley & Sons
Language eng
Formatted abstract
Genetical genomics, a novel approach combining microarray technology and quantitative genetic analysis, aims to identify the expression quantitative trait loci (eQTLs), which may regulate the genome-wide expression pattern. In this article, we have studied yeast genomic eQTL data to investigate how the genetic eQTL regulation of ancestral gene has diverged since gene duplication. Our findings are as follows: (i) Duplicate genes have higher heritability for gene expression than single-copy genes, but little difference in their epistasis and directional effect. (ii) The divergence of trans-acting eQTLs between duplicate pairs increases with the evolutionary time since gene duplication. (iii) Trans-acting eQTL divergence can explain about 21% of the variation in expression divergence between duplicate pairs with KS<2.0, which increases to 27% when the transcription factor (TF)–target interaction divergence is combined. Moreover, under the partial correlation analysis, trans-acting eQTL divergence seems make a bigger contribution to expression divergence than does TF divergence. (iv) Trans-acting eQTL divergence between duplicate pairs is correlated with gene ontology categories “Biological processes” and “Cellular components,” but not with “Molecular functions,” and is related to fitness defect under treatment conditions, but not with fitness under normal condition. We conclude that eQTL analysis provides a novel approach to explore the effect of gene duplications on the genetic regulatory network.
Keyword Transcriptional regulation
Saccharomyces-cerevisiae
Expression profiles
Natural-populations
Protein evolution
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Brain Institute Publications
 
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