Hidden layers of human small RNAs

Hideya Kawaji¹^,2^,3 , Mari Nakamura² , Yukari Takahashi¹^,2 , Albin Sandelin⁴ , Shintaro Katayama² , Shiro Fukuda² , Carsten O Daub² , Chikatoshi Kai² , Jun Kawai² , Jun Yasuda¹^,2 , Piero Carninci⁵ and Yoshihide Hayashizaki¹^,2^,5

¹Functional RNA Research Program, RIKEN Frontier Research System, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

²Genome Exploration Research Group, RIKEN Genomic Sciences Center(GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

³NTT Software Corporation, Teisan Kannai Bldg. 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan

⁴The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2100 København ∅, Denmark

⁵Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

author email corresponding author email

BMC Genomics 2008, 9:157doi:10.1186/1471-2164-9-157


Published:	10 April 2008

Abstract

Background

Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs.

Results

Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19–40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs) suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs.

Conclusion

Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.