title: Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus.
abstract: Small RNAs constitute a new and unanticipated layer of gene regulation present in the three domains of life. In plants, all organs are ultimately derived from a few pluripotent stem cells localized in specialized structures called apical meristems. The development of meristems involves a coordinated balance between undifferentiated growth and differentiation, a phenomenon requiring a tight regulation of gene expression. We used in vitro cultured embryogenic calli as a model to investigate the roles of meristem-associated small RNAs. Using high throughput sequencing, we sequenced 20 million short reads with size of 18-30 nt from rice undifferentiated and differentiated calli. We confirmed 50 known microRNA families, representing one third of annotated rice microRNAs. Using a specific computational pipeline for plant microRNA identification, we identified 24 novel microRNA families. Among them, 53 microRNA or microRNA* sequences appear to vary in expression between differentiated and undifferentiated calli, suggesting a role in meristem development. Our analysis also revealed a new class of plant small RNAs derived from 5' or 3' ends of mature tRNA analogous to the tRFs in human cancer cell. We independently verified the expression of these small RNAs from 5' end of mature tRNA using qRT-PCR.
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, PR China.
authors.forename: Chong-Jian
authors.initials: CJ
authors.lastname: Chen
authors.forename: Qing
authors.initials: Q
authors.lastname: liu
authors.forename: Yu-Chan
authors.initials: YC
authors.lastname: Zhang
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
authors.forename: Yue-Qin
authors.initials: YQ
authors.lastname: Chen
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
mesh_terms: D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018519:Meristem / Q000378:metabolism; D035683:MicroRNAs / Q000032:analysis*; D008969:Molecular Sequence Data; D012275:Oryza / Q000196:embryology* / Q000235:genetics*; D018749:RNA, Plant / Q000032:analysis*; D034741:RNA, Small Interfering / Q000032:analysis*; D012343:RNA, Transfer / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering; D012343:RNA, Transfer