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Cis-regulatory change and expression divergence between duplicate genes formed by genome duplication of Arabidopsis thaliana

  • Article
  • Special Topic Bioinformatics
  • Published:
Chinese Science Bulletin

Abstract

As an index of functional divergence, expression divergence between duplicate gene copies has been observed and correlated with protein coding sequence divergence and bias in gene functional classes. However, the changes in the cis-regulatory region of the duplicate genes which is thought to have important role in expression divergence, has not been explored on the genome-wide scale. We analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. The divergence in cis-regulatory regions between two copies is positively correlated with the magnitude difference of expression. Moreover, we find that highly expressed duplicate gene pairs have a more diverged cis-regulatory region than weakly expressed gene pairs. We also show that the correlation between expression functional constraint and protein functional constraint is different in old and young duplicate pairs. Our results suggest that cis-regulatory sequence divergence contributes to the expression divergence of duplicate genes formed by genome-wide duplication. Cis-regulatory region diverges faster in highly expressed duplicate pairs. The diversify selection strengths that act on cis-regulatory region and protein coding region are negatively correlated in young duplicate pairs under expression constraint.

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Authors and Affiliations

  1. State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, 510275, China

    KeNian Chen, Tian Tang & SuHua Shi

  2. Department of Biotechnology, Guangzhou Medical College, Guangzhou, 510182, China

    KeNian Chen

  3. College of Computer Science, Hangzhou Dianzi University, Hangzhou, 310018, China

    YanBin Zhang

Authors
  1. KeNian Chen
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  2. YanBin Zhang
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  3. Tian Tang
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  4. SuHua Shi
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Correspondence to SuHua Shi.

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Chen, K., Zhang, Y., Tang, T. et al. Cis-regulatory change and expression divergence between duplicate genes formed by genome duplication of Arabidopsis thaliana. Chin. Sci. Bull. 55, 2359–2365 (2010). https://doi.org/10.1007/s11434-010-3027-5

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  • DOI: https://doi.org/10.1007/s11434-010-3027-5

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