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Science
Vol. 321 no. 5891 pp. 956-960
DOI: 10.1126/science.1160342
  • Report

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

  1. Marie-Laure Yaspo1,
  1. 1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
  2. 2 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
  3. 3 International Max Planck Research School for Computational Biology and Scientific Computing.
  4. 4 Genomatix Software Gmbh, Bayerstrasse 85a, 80335 Munich, Germany.
  1. To whom correspondence should be addressed. E-mail: yaspo{at}molgen.mpg.de
  • * These authors contributed equally to this work.

Abstract

The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis of known transcripts, RNA-Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing.

    • Received for publication 12 May 2008.
    • Accepted for publication 27 June 2008.