IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v458y2009i7235d10.1038_nature07672.html
   My bibliography  Save this article

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Author

Listed:
  • Mitchell Guttman

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Department of Biology,)

  • Ido Amit

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Manuel Garber

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Courtney French

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Michael F. Lin

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • David Feldser

    (The Koch Institute for Integrative Cancer Research,)

  • Maite Huarte

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA)

  • Or Zuk

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Bryce W. Carey

    (Department of Biology,
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • John P. Cassady

    (Department of Biology,
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Moran N. Cabili

    (Harvard Medical School, Boston, Massachusetts 02114, USA)

  • Rudolf Jaenisch

    (Department of Biology,
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Tarjei S. Mikkelsen

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    and)

  • Tyler Jacks

    (Department of Biology,
    The Koch Institute for Integrative Cancer Research,)

  • Nir Hacohen

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Center for Immunology and Inflammatory Diseases,)

  • Bradley E. Bernstein

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
    Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Manolis Kellis

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA)

  • Aviv Regev

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Department of Biology,)

  • John L. Rinn

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
    Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Eric S. Lander

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Department of Biology,
    Harvard Medical School, Boston, Massachusetts 02114, USA
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

Abstract

Large RNAs: conserved for a purpose Mammalian genomes are transcribed to produce numerous large non-coding RNAs, but their function is unclear, primarily because these transcripts show little or no evidence of evolutionary conservation. A new approach to characterizing these mysterious molecules has now moved the field on. Rather than targeting the RNA molecules themselves, their existence was revealed as chromatin modifications or epigenomic marks in the DNA of four mouse cell types. The search yielded over a thousand large multi-exonic transcriptional units that do not overlap known protein-coding loci and are highly conserved. Possible functions could be assigned to each of these large intervening non-coding RNAs (or lincRNAs), ranging from embryonic stem cell pluripotency to cell proliferation. Specific lincRNAs turn out to be regulated by transcription factors that are key in these processes including p53, NFκB, Sox2, Oct4, and Nanog — and most of these lincRNAs are conserved across mammals.

Suggested Citation

  • Mitchell Guttman & Ido Amit & Manuel Garber & Courtney French & Michael F. Lin & David Feldser & Maite Huarte & Or Zuk & Bryce W. Carey & John P. Cassady & Moran N. Cabili & Rudolf Jaenisch & Tarjei S, 2009. "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals," Nature, Nature, vol. 458(7235), pages 223-227, March.
    • Handle: RePEc:nat:nature:v:458:y:2009:i:7235:d:10.1038_nature07672
    DOI: 10.1038/nature07672
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature07672
    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/nature07672?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. Dandan Wang & Shengnan Wang & Wenjie Tian & Yuehui Ma & Lin Jiang, 2022. "Comprehensive Analysis of lncRNA and mRNA Reveals the Effect of ZBED6 on Spleen Growth in Pigs," Agriculture, MDPI, vol. 13(1), pages 1-13, December.
    2. Siddharth Sethi & David Zhang & Sebastian Guelfi & Zhongbo Chen & Sonia Garcia-Ruiz & Emmanuel O. Olagbaju & Mina Ryten & Harpreet Saini & Juan A. Botia, 2022. "Leveraging omic features with F3UTER enables identification of unannotated 3’UTRs for synaptic genes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Qiwen Deng & Huiling Sun & Bangshun He & Yuqin Pan & Tianyi Gao & Jie Chen & Houqun Ying & Xian Liu & Feng Wang & Yong Xu & Shukui Wang, 2014. "Prognostic Value of Long Non-Coding RNA HOTAIR in Various Cancers," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-9, October.
    4. Lei Sun & Hui Liu & Lin Zhang & Jia Meng, 2015. "lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-16, October.
    5. Kroll, K.M. & Ferrantini, A. & Domany, E., 2010. "Introduction to biology and chromosomal instabilities in cancer," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(20), pages 4374-4388.

    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:458:y:2009:i:7235:d:10.1038_nature07672. 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.