title: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
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.
authors.affiliation: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Sultan
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.forename: Hugues
authors.initials: H
authors.lastname: Richard
authors.forename: Alon
authors.initials: A
authors.lastname: Magen
authors.forename: Andreas
authors.initials: A
authors.lastname: Klingenhoff
authors.forename: Matthias
authors.initials: M
authors.lastname: Scherf
authors.forename: Martin
authors.initials: M
authors.lastname: Seifert
authors.forename: Tatjana
authors.initials: T
authors.lastname: Borodina
authors.forename: Aleksey
authors.initials: A
authors.lastname: Soldatov
authors.forename: Dmitri
authors.initials: D
authors.lastname: Parkhomchuk
authors.forename: Dominic
authors.initials: D
authors.lastname: Schmidt
authors.forename: Sean
authors.initials: S
authors.lastname: O'Keeffe
authors.forename: Stefan
authors.initials: S
authors.lastname: Haas
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Yaspo
mesh_terms: D017398:Alternative Splicing; D002460:Cell Line; D045744:Cell Line, Tumor; D019295:Computational Biology; D018076:DNA, Complementary; D021901:DNA, Intergenic; D005091:Exons; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D007438:Introns; D020411:Oligonucleotide Array Sequence Analysis; D012319:RNA Polymerase II / Q000378:metabolism; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D018076:DNA, Complementary; D021901:DNA, Intergenic; D022821:RNA Splice Sites; D012333:RNA, Messenger; D012319:RNA Polymerase II