title: Cloning of novel repeat-associated small RNAs derived from hairpin precursors in Oryza sativa.
abstract: Plant small non-coding RNAs including microRNAs (miRNAs), small interfering RNAs (siRNAs) and trans-acting siRNAs, play important roles in modulating gene expression in cells. Here we isolated 21 novel endogenous small RNA molecules, ranging from 18 to 24 nucleotides, in Oryza sativa that can be mapped to 111 hairpin precursors. Further analysis indicated that most of these hairpin sequences originated from putative miniature inverted-repeat transposable elements, a major type of DNA transposon. Considering that miRNA is characteristic of hairpin-like precursor and plant endogenous siRNAs are often located at transposon regions, we hypothesized that our cloned small RNAs might represent the intermediate product in the evolutionary process between siRNAs and miRNAs. Northern blot analysis indicated that five of them were much more abundantly expressed in flower compared to other tissues, implying their potential function in inflorescence. In conclusion, our results enrich rice small RNA data and provide a meaningful perspective for small RNA annotation in plants.
authors.affiliation: State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Chengguo
authors.initials: C
authors.lastname: Yao
authors.forename: Botao
authors.initials: B
authors.lastname: Zhao
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.forename: Wenming
authors.initials: W
authors.lastname: Qin
authors.forename: Bing
authors.initials: B
authors.lastname: Huang
authors.forename: Youxin
authors.initials: Y
authors.lastname: Jin
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering