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Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Author

Listed:
  • Alexander Stark

    (The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

  • Michael F. Lin

    (The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

  • Pouya Kheradpour

    (Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

  • Jakob S. Pedersen

    (The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA)

  • Leopold Parts

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Institute of Computer Science, University of Tartu)

  • Joseph W. Carlson

    (BDGP, LBNL, 1 Cyclotron Road MS 64-0119, Berkeley, California 94720, USA)

  • Madeline A. Crosby

    (FlyBase, The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA)

  • Matthew D. Rasmussen

    (Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

  • Sushmita Roy

    (University of New Mexico, Albuquerque, New Mexico 87131, USA)

  • Ameya N. Deoras

    (Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

  • J. Graham Ruby

    (MIT, Cambridge, Massachusetts 02139, USA
    Whitehead Institute, Cambridge, Massachusetts 02142, USA)

  • Julius Brennecke

    (Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA)

  • Emily Hodges

    (Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA)

  • Angie S. Hinrichs

    (Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA)

  • Anat Caspi

    (University of California, San Francisco/University of California, Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 97210, USA)

  • Benedict Paten

    (Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    EMBL Nucleotide Sequence Submissions, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • Seung-Won Park

    (G-629, MSB, 185 South Orange Avenue, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA)

  • Mira V. Han

    (Indiana University)

  • Morgan L. Maeder

    (Connecticut College, New London, Connecticut 06320, USA)

  • Benjamin J. Polansky

    (Connecticut College, New London, Connecticut 06320, USA)

  • Bryanne E. Robson

    (Connecticut College, New London, Connecticut 06320, USA)

  • Stein Aerts

    (Laboratory of Neurogenetics, VIB, 3000 Leuven, Belgium
    K. U. Leuven School of Medicine)

  • Jacques van Helden

    (Universite Libre de Bruxelles)

  • Bassem Hassan

    (Laboratory of Neurogenetics, VIB, 3000 Leuven, Belgium
    K. U. Leuven School of Medicine)

  • Donald G. Gilbert

    (Indiana University, Bloomington, Indiana 47405, USA)

  • Deborah A. Eastman

    (Connecticut College, New London, Connecticut 06320, USA)

  • Michael Rice

    (Wesleyan University, Middletown, Connecticut 06459, USA)

  • Michael Weir

    (Wesleyan University Middletown)

  • Matthew W. Hahn

    (Indiana University)

  • Yongkyu Park

    (G-629, MSB, 185 South Orange Avenue, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA)

  • Colin N. Dewey

    (University of Wisconsin-Madison, Madison, Wisconsin 53706, USA)

  • Lior Pachter

    (University of California at Berkeley, Berkeley, California 94720, USA
    University of California at Berkeley, Berkeley, California 94720, USA)

  • W. James Kent

    (Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA)

  • David Haussler

    (Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA)

  • Eric C. Lai

    (Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA)

  • David P. Bartel

    (MIT, Cambridge, Massachusetts 02139, USA
    Whitehead Institute, Cambridge, Massachusetts 02142, USA)

  • Gregory J. Hannon

    (Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA)

  • Thomas C. Kaufman

    (Indiana University, Bloomington, Indiana 47405, USA)

  • Michael B. Eisen

    (Graduate Group in Biophysics, and Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA)

  • Andrew G. Clark

    (Cornell University, Ithaca, New York 14853, USA)

  • Douglas Smith

    (Agencourt Bioscience Corporation, 500 Cummings Center, Suite 2450, Beverly, Massachusetts 01915, USA)

  • Susan E. Celniker

    (BDGP, LBNL, 1 Cyclotron Road MS 64-0119, Berkeley, California 94720, USA)

  • William M. Gelbart

    (FlyBase, The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Harvard University, Cambridge, Massachusetts 02138, USA)

  • Manolis Kellis

    (The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA)

Abstract

Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or ‘evolutionary signatures’, dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.

Suggested Citation

  • Alexander Stark & Michael F. Lin & Pouya Kheradpour & Jakob S. Pedersen & Leopold Parts & Joseph W. Carlson & Madeline A. Crosby & Matthew D. Rasmussen & Sushmita Roy & Ameya N. Deoras & J. Graham Rub, 2007. "Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures," Nature, Nature, vol. 450(7167), pages 219-232, November.
    • Handle: RePEc:nat:nature:v:450:y:2007:i:7167:d:10.1038_nature06340
    DOI: 10.1038/nature06340
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