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A cis-regulatory map of the Drosophila genome

Author

Listed:
  • Nicolas Nègre

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Christopher D. Brown

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Lijia Ma

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Christopher Aaron Bristow

    (Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard)

  • Steven W. Miller

    (University of California San Diego)

  • Ulrich Wagner

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Pouya Kheradpour

    (Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard)

  • Matthew L. Eaton

    (Duke University Medical Center)

  • Paul Loriaux

    (Signaling Systems Laboratory, University of California, San Diego, 9500 Gilman Drive)

  • Rachel Sealfon

    (Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard)

  • Zirong Li

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Haruhiko Ishii

    (University of California San Diego)

  • Rebecca F. Spokony

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Jia Chen

    (National Center for Data Mining, University of Illinois at Chicago)

  • Lindsay Hwang

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Chao Cheng

    (Program in Computational Biology & Bioinformatics, Yale University
    Yale University
    Yale University)

  • Richard P. Auburn

    (University of Cambridge)

  • Melissa B. Davis

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Marc Domanus

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Parantu K. Shah

    (Dana-Farber Cancer Institute, Harvard School of Public Health)

  • Carolyn A. Morrison

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Jennifer Zieba

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Sarah Suchy

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Lionel Senderowicz

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Alec Victorsen

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • Nicholas A. Bild

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • A. Jason Grundstad

    (Institute for Genomics and Systems Biology, The University of Chicago)

  • David Hanley

    (National Center for Data Mining, University of Illinois at Chicago)

  • David M. MacAlpine

    (Duke University Medical Center)

  • Mattias Mannervik

    (Wenner-Gren Institute, Arrhenius Laboratories E3, Stockholm University)

  • Koen Venken

    (BCM)

  • Hugo Bellen

    (BCM)

  • Robert White

    (Development and Neuroscience, University of Cambridge)

  • Mark Gerstein

    (Program in Computational Biology & Bioinformatics, Yale University
    Yale University)

  • Steven Russell

    (University of Cambridge)

  • Robert L. Grossman

    (Institute for Genomics and Systems Biology, The University of Chicago
    National Center for Data Mining, University of Illinois at Chicago
    University of Chicago)

  • Bing Ren

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    Institute of Genomic Medicine & Moores Cancer Center, 9500 Gilman Drive)

  • James W. Posakony

    (University of California San Diego)

  • Manolis Kellis

    (Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard)

  • Kevin P. White

    (Institute for Genomics and Systems Biology, The University of Chicago)

Abstract

Elements of gene function Three papers in this issue of Nature report on the modENCODE initiative, which aims to characterize functional DNA elements in the fruitfly Drosophila melanogaster and the roundworm Caenorhabditis elegans. Kharchenko et al. present a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. They describe nine prevalent chromatin states. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. Graveley et al. have used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events. Finally, Nègre et al. have produced a map of the regulatory part of the fruitfly genome, defining a vast array of putative regulatory elements, such as enhancers, promoters, insulators and silencers.

Suggested Citation

  • Nicolas Nègre & Christopher D. Brown & Lijia Ma & Christopher Aaron Bristow & Steven W. Miller & Ulrich Wagner & Pouya Kheradpour & Matthew L. Eaton & Paul Loriaux & Rachel Sealfon & Zirong Li & Haruh, 2011. "A cis-regulatory map of the Drosophila genome," Nature, Nature, vol. 471(7339), pages 527-531, March.
    • Handle: RePEc:nat:nature:v:471:y:2011:i:7339:d:10.1038_nature09990
    DOI: 10.1038/nature09990
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    Cited by:

    1. Kenneth A. Wilson & Sudipta Bar & Eric B. Dammer & Enrique M. Carrera & Brian A. Hodge & Tyler A. U. Hilsabeck & Joanna Bons & George W. Brownridge & Jennifer N. Beck & Jacob Rose & Melia Granath-Pane, 2024. "OXR1 maintains the retromer to delay brain aging under dietary restriction," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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