IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v466y2010i7303d10.1038_nature09165.html
   My bibliography  Save this article

Conserved role of intragenic DNA methylation in regulating alternative promoters

Author

Listed:
  • Alika K. Maunakea

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco
    Present addresses: Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland 20892, USA (A.K.M.); EPFL-ISREC, SV 2818, Station 19, Lausanne 1015, Switzerland (K.S.).)

  • Raman P. Nagarajan

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco)

  • Mikhail Bilenky

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Tracy J. Ballinger

    (Center for Biomolecular Science and Engineering, University of California)

  • Cletus D’Souza

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Shaun D. Fouse

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco)

  • Brett E. Johnson

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco)

  • Chibo Hong

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco)

  • Cydney Nielsen

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Yongjun Zhao

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Gustavo Turecki

    (McGill Group for Suicide Studies, Douglas Hospital Research Centre, 6875 LaSalle Blvd, Verdun, Quebec H4H 1R3, Canada)

  • Allen Delaney

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Richard Varhol

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Nina Thiessen

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Ksenya Shchors

    (University of California San Francisco
    Present addresses: Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland 20892, USA (A.K.M.); EPFL-ISREC, SV 2818, Station 19, Lausanne 1015, Switzerland (K.S.).)

  • Vivi M. Heine

    (University of California San Francisco)

  • David H. Rowitch

    (University of California San Francisco)

  • Xiaoyun Xing

    (Center for Genome Sciences and Systems Biology, Washington University)

  • Chris Fiore

    (Center for Genome Sciences and Systems Biology, Washington University)

  • Maximiliaan Schillebeeckx

    (Center for Genome Sciences and Systems Biology, Washington University)

  • Steven J. M. Jones

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • David Haussler

    (Center for Biomolecular Science and Engineering, University of California
    Howard Hughes Medical Institute, University of California)

  • Marco A. Marra

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Martin Hirst

    (Genome Sciences Centre, BC Cancer Agency, 675 W. 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada)

  • Ting Wang

    (Center for Biomolecular Science and Engineering, University of California
    Center for Genome Sciences and Systems Biology, Washington University)

  • Joseph F. Costello

    (Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco)

Abstract

Methylation in the genes DNA methylation plays an important role in the maintenance of cell identity through its effect on gene expression. Methylation of 5′ promoters is known to suppress gene expression, while the role of intragenic DNA methylation — where methylation occurs within the body of a gene itself — has been less extensively studied and remains controversial. A map of DNA methylation from the human brain has now been constructed with unprecedented coverage using next-generation sequencing. Integration of this map with brain tissue ChIP-sequencing for histone methylation, and gene expression in mouse and human, highlights a major role for intragenic methylation in regulating tissue-specific promoters in gene bodies, and a surprisingly minor role in 5′ promoters.

Suggested Citation

  • Alika K. Maunakea & Raman P. Nagarajan & Mikhail Bilenky & Tracy J. Ballinger & Cletus D’Souza & Shaun D. Fouse & Brett E. Johnson & Chibo Hong & Cydney Nielsen & Yongjun Zhao & Gustavo Turecki & Alle, 2010. "Conserved role of intragenic DNA methylation in regulating alternative promoters," Nature, Nature, vol. 466(7303), pages 253-257, July.
    • Handle: RePEc:nat:nature:v:466:y:2010:i:7303:d:10.1038_nature09165
    DOI: 10.1038/nature09165
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature09165
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature09165?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

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


    Cited by:

    1. Chirag Nepal & Jesper B. Andersen, 2023. "Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Rahul Kumar & Prashant Swapnil & Mukesh Meena & Shweta Selpair & Bal Govind Yadav, 2022. "Plant Growth-Promoting Rhizobacteria (PGPR): Approaches to Alleviate Abiotic Stresses for Enhancement of Growth and Development of Medicinal Plants," Sustainability, MDPI, vol. 14(23), pages 1-16, November.
    3. Nicholas C. Gervais & Rebecca S. Shapiro, 2024. "Discovering the hidden function in fungal genomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. David Martino & Nina Kresoje & Nelly Amenyogbe & Rym Ben-Othman & Bing Cai & Mandy Lo & Olubukola Idoko & Oludare A. Odumade & Reza Falsafi & Travis M. Blimkie & Andy An & Casey P. Shannon & Sebastian, 2024. "DNA Methylation signatures underpinning blood neutrophil to lymphocyte ratio during first week of human life," Nature Communications, Nature, vol. 15(1), pages 1-14, 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:nature:v:466:y:2010:i:7303:d:10.1038_nature09165. 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.