Hidden layers of human small RNAs.
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.


CONCLUSIONS
Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
Kawaji
Hideya
H
Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. kawaji@gsc.riken.jp
Nakamura
Mari
M
Takahashi
Yukari
Y
Sandelin
Albin
A
Katayama
Shintaro
S
Fukuda
Shiro
S
Daub
Carsten O
CO
Kai
Chikatoshi
C
Kawai
Jun
J
Yasuda
Jun
J
Carninci
Piero
P
Hayashizaki
Yoshihide
Y
D020029:Base Pairing; D001483:Base Sequence; D015152:Blotting, Northern; D019143:Evolution, Molecular; D015723:Gene Library; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D012313:RNA / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
D012313:RNA