A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
- Marc Sultan1,*,
- Marcel H. Schulz2,3,*,
- Hugues Richard2,*,
- Alon Magen1,
- Andreas Klingenhoff4,
- Matthias Scherf4,
- Martin Seifert4,
- Tatjana Borodina1,
- Aleksey Soldatov1,
- Dmitri Parkhomchuk1,
- Dominic Schmidt1,
- Sean O'Keeffe2,
- Stefan Haas2,
- Martin Vingron2,
- Hans Lehrach1,
- Marie-Laure Yaspo1,†
- 1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
- 2 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
- 3 International Max Planck Research School for Computational Biology and Scientific Computing.
- 4 Genomatix Software Gmbh, Bayerstrasse 85a, 80335 Munich, Germany.
- ↵† To whom correspondence should be addressed. E-mail:
↵* These authors contributed equally to this work.
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.