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Genome Res. 13:1301-1306, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/03 $5.00
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Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

Koji Numata1,2, Akio Kanai2, Rintaro Saito2,4, Shinji Kondo4, Jun Adachi4, Laurens G. Wilming6, David A. Hume7, RIKEN GER Group4, GSL Members5,8, Yoshihide Hayashizaki4,5 and Masaru Tomita2,3,9

1Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, Kanagawa 252-8520, Japan 2Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan 3Department of Environmental Information, Keio University, Fujisawa, Kanagawa 252-8520, Japan 4Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan 5Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan 6Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK 7Institute for Molecular Bioscience and School of Molecular and Microbial Sciences, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia

With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)—RNA molecules that are not translated to protein products—has become more evident. A subclass of ncRNA transcripts are encoded by highly regulated, multi-exon, transcriptional units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering approach. We initially searched for previously reported ncRNAs and found nine murine ncRNAs and homologs of several previously described nonmouse ncRNAs. Through our computational approach to filter artifact-free clones that lack protein coding potential, we extracted 4280 transcripts as the largest-candidate set. Many clones in the set had EST hits, potential CpG islands surrounding the transcription start sites, and homologies with the human genome. This implies that many candidates are indeed transcribed in a regulated manner. Our results demonstrate that ncRNAs are a major functional subclass of processed transcripts in mammals.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1011603.

8 Takahiro Arakawa, Piero Carninci, and Jun Kawai.

9 Corresponding author.
E-MAIL mt{at}sfc.keio.ac.jp; FAX 81 (466) 47-5099.

[Supplemental material is available online at www.genome.org.]


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