IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v10y2019i1d10.1038_s41467-019-10026-1.html
   My bibliography  Save this article

DNA methylation repels targeting of Arabidopsis REF6

Author

Listed:
  • Qi Qiu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Hailiang Mei

    (Chinese Academy of Sciences)

  • Xian Deng

    (Chinese Academy of Sciences)

  • Kaixuan He

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Baixing Wu

    (Fudan University)

  • Qingqing Yao

    (Fudan University)

  • Jixiang Zhang

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Falong Lu

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jinbiao Ma

    (Fudan University)

  • Xiaofeng Cao

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

Abstract

RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.

Suggested Citation

  • Qi Qiu & Hailiang Mei & Xian Deng & Kaixuan He & Baixing Wu & Qingqing Yao & Jixiang Zhang & Falong Lu & Jinbiao Ma & Xiaofeng Cao, 2019. "DNA methylation repels targeting of Arabidopsis REF6," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10026-1
    DOI: 10.1038/s41467-019-10026-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-019-10026-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-019-10026-1?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. Lindo, Jason M. & Pineda-Torres, Mayra, 2021. "New Evidence on the Effects of Mandatory Waiting Periods for Abortion," Journal of Health Economics, Elsevier, vol. 80(C).

    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:10:y:2019:i:1:d:10.1038_s41467-019-10026-1. 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.