Antisense transcripts with FANTOM2 clone set and their implications for gene regulation

Hidenori Kiyosawa, Itaru Yamanaka, Naoki Osato, Shinji Kondo, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki

Research output: Contribution to journalReview articlepeer-review

201 Citations (Scopus)

Abstract

We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sense-antisense transcript and nonantisense bidirectional transcription pairs in mammals. The FANTOM2 cDNA set appears to contain substantially large numbers of noncoding transcripts suitable for antisense transcript analysis. The average proportion of loci encoding sense-antisense transcript and nonantisense bidirectional transcription pairs on autosomes was 15.1 and 5.4%, respectively. Those on the X chromosome were 6.3 and 4.2%, respectively. Sense-antisense transcript pairs, rather than nonantisense bidirectional transcription pairs, may be less prevalent on the X chromosome, possibly due to X chromosome inactivation. Sense and antisense transcripts tended to be isolated from the same libraries, where nonantisense bidirectional transcription pairs were not apparently coregulated. The existence of large numbers of natural antisense transcripts implies that the regulation of gene expression by antisense transcripts is more common that previously recognized. The viewer showing mapping patterns of sense-antisense transcript pairs and nonantisense bidirectional transcription pairs on the genome and other related statistical data is available on our Web site.

Original languageEnglish
Pages (from-to)1324-1334
Number of pages11
JournalGenome Research
Volume13
Issue number6 B
DOIs
Publication statusPublished - 2003 Jun 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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