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Genome Res. 13:1324-1334, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/03 $5.00
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Letter

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

Hidenori Kiyosawa1,2,4, Itaru Yamanaka1, Naoki Osato1, Shinji Kondo1 RIKEN GER Group1 GSLMembers3,5 and Yoshihide Hayashizaki1,2,3,6

1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan 2Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan 3Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

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.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.982903.

4 Present address: RIKEN Tsukuba Institute, BioResource Center (BRC), Tsukuba, Ibaraki, 305-0074, Japan.

5 Takahiro Arakawa, Piero Carninci, and Jun Kawai.

6 Corresponding author.
E-MAIL yosihide{at}gsc.riken.go.jp; FAX 45-5039216.


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