Hidden layers of human small RNAs

@article{citeulike:2649058, 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.}, author = {Kawaji, Hideya and Nakamura, Mari and Takahashi, Yukari and Sandelin, Albin and Katayama, Shintaro and Fukuda, Shiro and Daub, Carsten and Kai, Chikatoshi and Kawai, Jun and Yasuda, Jun and Carninci, Piero and Hayashizaki, Yoshihide }, citeulike-article-id = {2649058}, doi = {http://dx.doi.org/10.1186/1471-2164-9-157}, journal = {BMC Genomics}, keywords = {microrna, rna, sirna}, number = {1}, posted-at = {2008-04-23 04:27:28}, priority = {2}, title = {Hidden layers of human small RNAs}, url = {http://dx.doi.org/10.1186/1471-2164-9-157}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2649058 L3 - citeulike-article-id:2649058 TI - Hidden layers of human small RNAs JF - BMC Genomics VL - 9 IS - 1 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. CONCLUSIONS:Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs. KW - microrna KW - rna KW - sirna AU - Kawaji, Hideya AU - Nakamura, Mari AU - Takahashi, Yukari AU - Sandelin, Albin AU - Katayama, Shintaro AU - Fukuda, Shiro AU - Daub, Carsten AU - Kai, Chikatoshi AU - Kawai, Jun AU - Yasuda, Jun AU - Carninci, Piero AU - Hayashizaki, Yoshihide PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2164-9-157 ER -