title: Hidden layers of human small RNAs.
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.
  
  
  CONCLUSIONS
  Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
authors.affiliation: Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. kawaji@gsc.riken.jp
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Mari
authors.initials: M
authors.lastname: Nakamura
authors.forename: Yukari
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.forename: Shiro
authors.initials: S
authors.lastname: Fukuda
authors.forename: Carsten O
authors.initials: CO
authors.lastname: Daub
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Jun
authors.initials: J
authors.lastname: Yasuda
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: 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
chemical_list: D012313:RNA