title: Global identification of human transcribed sequences with genome tiling arrays.
abstract: Elucidating the transcribed regions of the genome constitutes a fundamental aspect of human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome. Transcribed sequences were located across the genome via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained from human liver tissue. In addition to identifying many known and predicted genes, we found 10,595 transcribed sequences not detected by other methods. A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Bertone
authors.forename: Viktor
authors.initials: V
authors.lastname: Stolc
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Royce
authors.forename: Joel S
authors.initials: JS
authors.lastname: Rozowsky
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Urban
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhu
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Waraporn
authors.initials: W
authors.lastname: Tongprasit
authors.forename: Manoj
authors.initials: M
authors.lastname: Samanta
authors.forename: Sherman
authors.initials: S
authors.lastname: Weissman
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D018899:CpG Islands; D018076:DNA, Complementary; D021901:DNA, Intergenic; D030541:Databases, Genetic; D005091:Exons; D015894:Genome, Human; D006801:Humans; D007438:Introns; D051379:Mice; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D021901:DNA, Intergenic; D015345:Oligonucleotide Probes; D011506:Proteins; D012333:RNA, Messenger