Global identification of human transcribed sequences with genome tiling arrays.
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.
Bertone
Paul
P
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.
Stolc
Viktor
V
Royce
Thomas E
TE
Rozowsky
Joel S
JS
Urban
Alexander E
AE
Zhu
Xiaowei
X
Rinn
John L
JL
Tongprasit
Waraporn
W
Samanta
Manoj
M
Weissman
Sherman
S
Gerstein
Mark
M
Snyder
Michael
M
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
D018076:DNA, Complementary; D021901:DNA, Intergenic; D015345:Oligonucleotide Probes; D011506:Proteins; D012333:RNA, Messenger