title: A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa.
abstract: Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5' and 3' termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.
authors.affiliation: Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Liu
authors.forename: Danmeng
authors.initials: D
authors.lastname: Zhu
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Guangming
authors.initials: G
authors.lastname: He
authors.forename: Baoyan
authors.initials: B
authors.lastname: Bai
authors.forename: Yijun
authors.initials: Y
authors.lastname: Qi
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated