IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v3y2012i1d10.1038_ncomms1954.html
   My bibliography  Save this article

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

Author

Listed:
  • Xiaoli Shi

    (Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, One University Station, A4800, Austin, Texas 78712, USA.)

  • Danny W-K. Ng

    (Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, One University Station, A4800, Austin, Texas 78712, USA.)

  • Changqing Zhang

    (Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, One University Station, A4800, Austin, Texas 78712, USA.)

  • Luca Comai

    (Plant Biology and Genome Center, University of California, 451 Health Sciences Drive, Davis, Davis, California 95616, USA.)

  • Wenxue Ye

    (State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University)

  • Z. Jeffrey Chen

    (Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, One University Station, A4800, Austin, Texas 78712, USA.
    State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University)

Abstract

Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, cis- and trans-regulation is associated with chromatin modifications. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.

Suggested Citation

  • Xiaoli Shi & Danny W-K. Ng & Changqing Zhang & Luca Comai & Wenxue Ye & Z. Jeffrey Chen, 2012. "Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
  • Handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms1954
    DOI: 10.1038/ncomms1954
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms1954
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/ncomms1954?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Fei He & Wei Wang & William B. Rutter & Katherine W. Jordan & Jie Ren & Ellie Taagen & Noah DeWitt & Deepmala Sehgal & Sivakumar Sukumaran & Susanne Dreisigacker & Matthew Reynolds & Jyotirmoy Halder , 2022. "Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms1954. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.