Hidden layers of human small RNAs

TY - JOUR

T1 - Hidden layers of human small RNAs

AU - Kawaji, Hideya

AU - Nakamura, Mari

AU - Takahashi, Yukari

AU - Sandelin, Albin

AU - Katayama, Shintaro

AU - Fukuda, Shiro

AU - Daub, Carsten O

AU - Kai, Chikatoshi

AU - Kawai, Jun

AU - Yasuda, Jun

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

N1 - Keywords: Base Pairing; Base Sequence; Blotting, Northern; Evolution, Molecular; Gene Library; Humans; Molecular Sequence Data; Multigene Family; RNA; Sequence Alignment; Sequence Analysis, RNA

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

U2 - 10.1186/1471-2164-9-157

DO - 10.1186/1471-2164-9-157

M3 - Journal article

C2 - 18402656

SN - 1471-2164

VL - 9

SP - 157

JO - BMC Genomics

JF - BMC Genomics

ER -