Widespread occurrence of antisense transcription in the human genome.
An increasing number of eukaryotic genes are being found to have naturally occurring antisense transcripts. Here we study the extent of antisense transcription in the human genome by analyzing the public databases of expressed sequences using a set of computational tools designed to identify sense-antisense transcriptional units on opposite DNA strands of the same genomic locus. The resulting data set of 2,667 sense-antisense pairs was evaluated by microarrays containing strand-specific oligonucleotide probes derived from the region of overlap. Verification of specific cases by northern blot analysis with strand-specific riboprobes proved transcription from both DNA strands. We conclude that > or =60% of this data set, or approximately 1,600 predicted sense-antisense transcriptional units, are transcribed from both DNA strands. This indicates that the occurrence of antisense transcription, usually regarded as infrequent, is a very common phenomenon in the human genome. Therefore, antisense modulation of gene expression in human cells may be a common regulatory mechanism.
Yelin
Rodrigo
R
Compugen Ltd., 72 Pinchas Rosen St., Tel Aviv 69512, Israel.
Dahary
Dvir
D
Sorek
Rotem
R
Levanon
Erez Y
EY
Goldstein
Orly
O
Shoshan
Avi
A
Diber
Alex
A
Biton
Sharon
S
Tamir
Yael
Y
Khosravi
Rami
R
Nemzer
Sergey
S
Pinner
Elhanan
E
Walach
Shira
S
Bernstein
Jeanne
J
Savitsky
Kinneret
K
Rotman
Galit
G
D000465:Algorithms; D001483:Base Sequence; D016000:Cluster Analysis; D016373:DNA, Antisense / Q000235:genetics*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016372:RNA, Antisense / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics*; D014407:Tumor Cells, Cultured
D016373:DNA, Antisense; D016372:RNA, Antisense