Open Access Highly Accessed Research article

Hidden layers of human small RNAs

Hideya Kawaji123, Mari Nakamura2, Yukari Takahashi12, Albin Sandelin4, Shintaro Katayama2, Shiro Fukuda2, Carsten O Daub2, Chikatoshi Kai2, Jun Kawai2, Jun Yasuda12, Piero Carninci5* and Yoshihide Hayashizaki125

Author Affiliations

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

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

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

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

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

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

Published: 10 April 2008



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.


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.


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