title: Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors.
abstract: RNA silencing, mediated by small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs), is a potent antiviral or antibacterial mechanism, besides regulating normal cellular gene expression critical for development and physiology. To gain insights into host small RNA metabolism under infections by different viruses, we used Solexa/Illumina deep sequencing to characterize the small RNA profiles of rice plants infected by two distinct viruses, Rice dwarf virus (RDV, dsRNA virus) and Rice stripe virus (RSV, a negative sense and ambisense RNA virus), respectively, as compared with those from non-infected plants. Our analyses showed that RSV infection enhanced the accumulation of some rice miRNA*s, but not their corresponding miRNAs, as well as accumulation of phased siRNAs from a particular precursor. Furthermore, RSV infection also induced the expression of novel miRNAs in a phased pattern from several conserved miRNA precursors. In comparison, no such changes in host small RNA expression was observed in RDV-infected rice plants. Significantly RSV infection elevated the expression levels of selective OsDCLs and OsAGOs, whereas RDV infection only affected the expression of certain OsRDRs. Our results provide a comparative analysis, via deep sequencing, of changes in the small RNA profiles and in the genes of RNA silencing machinery induced by different viruses in a natural and economically important crop host plant. They uncover new mechanisms and complexity of virus-host interactions that may have important implications for further studies on the evolution of cellular small RNA biogenesis that impact pathogen infection, pathogenesis, as well as organismal development.
authors: Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
authors: Peng
authors: P
authors: Du
authors: Jianguo
authors: J
authors: Wu
authors: Jiayao
authors: J
authors: Zhang
authors: Shuqi
authors: S
authors: Zhao
authors: Hong
authors: H
authors: Zheng
authors: Ge
authors: G
authors: Gao
authors: Liping
authors: L
authors: Wei
authors: Yi
authors: Y
authors: Li
mesh_terms: D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D054884:Host-Pathogen Interactions; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000821:virology; D010935:Plant Diseases / Q000821:virology*; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D029364:Tenuivirus / Q000472:pathogenicity
chemical_list: D035683:MicroRNAs; D012330:RNA, Double-Stranded; D018749:RNA, Plant; D034741:RNA, Small Interfering