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Published Online July 3, 2008
Science DOI: 10.1126/science.1160342

Reports

Submitted on May 12, 2008
Accepted on June 26, 2008

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

Marc Sultan 1{dagger}, Marcel H. Schulz 2{dagger}, Hugues Richard 3{dagger}, Alon Magen 1, Andreas Klingenhoff 4, Matthias Scherf 4, Martin Seifert 4, Tatjana Borodina 1, Aleksey Soldatov 1, Dmitri Parkhomchuk 1, Dominic Schmidt 1, Sean O’Keeffe 3, Stefan Haas 3, Martin Vingron 3, Hans Lehrach 1, Marie-Laure Yaspo 1*

1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.
2 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.; International Max Planck Research School for Computational Biology and Scientific Computing.
3 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.
4 Genomatix Software Gmbh, Bayerstr. 85a, 80335 Munich, Germany.

* To whom correspondence should be addressed.
Marie-Laure Yaspo , E-mail: yaspo{at}molgen.mpg.de

{dagger}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. Shotgun sequencing of transcripts was used to generate randomly distributed reads. Of these, 50% mapped to unique genomic location, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to non-annotated genomic regions. Based on known transcripts, RNAseq can detect 25% more genes than microarrays. A global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing.


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