Advertisement
Perspective

Perspective The Perspective section provides experts with a forum to comment on topical or controversial issues of broad interest.

See all article types »

The Reality of Pervasive Transcription

  • Michael B. Clark,

    Affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

    X
  • Paulo P. Amaral equal contributor,

    equal contributor Contributed equally to this work with: Paulo P. Amaral, Felix J. Schlesinger

    Affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

    X
  • Felix J. Schlesinger equal contributor,

    equal contributor Contributed equally to this work with: Paulo P. Amaral, Felix J. Schlesinger

    Affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

    X
  • Marcel E. Dinger,

    Affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

    X
  • Ryan J. Taft,

    Affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

    X
  • John L. Rinn,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Chris P. Ponting,

    Affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

    X
  • Peter F. Stadler,

    Affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany

    X
  • Kevin V. Morris,

    Affiliation: Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California, United States of America

    X
  • Antonin Morillon,

    Affiliation: Institut Curie, UMR3244-Pavillon Trouillet Rossignol, Paris, France

    X
  • Joel S. Rozowsky,

    Affiliation: Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America

    X
  • Mark B. Gerstein,

    Affiliation: Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America

    X
  • Claes Wahlestedt,

    Affiliation: University of Miami, Miami, Florida, United States of America

    X
  • Yoshihide Hayashizaki,

    Affiliation: Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan

    X
  • Piero Carninci,

    Affiliation: Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan

    X
  • Thomas R. Gingeras mail,

    j.mattick@uq.edu.au(JSM); gingeras@cshl.edu (TRG)

    Affiliation: Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

    X
  • John S. Mattick mail

    j.mattick@uq.edu.au(JSM); gingeras@cshl.edu (TRG)

    Affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

    X
  • Published: July 12, 2011
  • DOI: 10.1371/journal.pbio.1000625

Reader Comments (1)

Post a new comment on this article

Estimate of "dark matter" RNA using single-molecule sequencing

Posted by pkapranov on 21 Jul 2011 at 02:04 GMT

Bravo Michael, John and Colleagues! To add to your findings we thought it important to bring everyone’s attention to a manuscript we published last year where we directly estimated the levels of “dark matter” RNAs in human cells and tissues using single-molecule sequencing of total RNA (http://www.ncbi.nlm.nih.g...). We reported the majority (up to ~2/3) of the mass of cellular RNA, after removing ribosomal and mitochondrial transcripts, corresponds to “dark matter” RNA population. This unique single molecule sequencing method for preparation of RNA does not rely on PCR amplification which can distort the cellular RNA profiles, thus differing significantly from all other RNAseq technologies. In addition, we found 100’s of very long (100’s of kbs) regions of abundant transcription in intergenic regions devoid of annotated transcripts; we termed these vlinc regions. Overall, we hope these works can finally put this long-raging debate about the complexity of the “dark matter” RNA and its relative cellular mass to rest. Our work, while not referred to by van Bakel et al and Clark et al, presents definitive information on the issues of selective expression and mass of these “dark matter” RNAs in normal and neoplastic cells.

Philipp Kapranov
Georges St. Laurent
Patrice Milos
Robert Arceci
John Thompson
Timothy Triche

Competing interests declared: I am a former employee and a consultant with Helicos BioSciences.