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nucleotide bias of DCL and AGO in plant anti-virus gene silencing

Protein & Cell 2010年第9期1卷 847-858页

作者： Thien Ho Liang Wang Linfeng Huang Zhigang Li Denise W.Pallett Tamas Dalmay Kazusato Ohshima John A.Walsh Hui Wang NERC/Centre for Ecology and Hydrology(CEH)Wallingford Maclean BuildingBenson LaneWallingfordOxfordshire OX108BBUK Department of Biochemistry University of OxfordSouth Parks RoadOxford OX13QUUK Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100029China School of Biological Sciences University of East AngliaNorwich NR47TJUK Laboratory of Plant Virology Faculty of AgricultureSaga University1-banchiHonjo-machiSaga 840-8502Japan Plant-Virus Interactions Group Warwick HRIWarwick UniversityWellesbourneWarwick CV359EFUK Current address:AF Building University of Dundee at SCRIInvergowrieDundee DD25DAUK Current address:Immune Disease Institute 200 Longwood AvenueBoston MA 02115USA

Plant Dicer-like(DCL)and Argonaute(AGO)are the key enzymes involved in anti-virus post-transcriptional gene silencing(AV-PTGS).Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA *** comparison with genome sequences of dicot-infecting Turnip mosaic virus(TuMV)and monocot-infecting Cocksfoot streak virus(CSV),viral-derived small interfering RNAs(vsiRNAs)displayed positive correlations between AV-PTGS efficiency and G+C content(GC%).Further investigations on nucleotide contents revealed that the vsiRNA populations had *** finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations,and AGO associated Arabidopsis endogenous siRNA populations,indicating that plant AGOs operated with *** further propose a hypothesis that AV-PTGS imposes selection pressure(s)on the evolution of plant *** hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination,suggesting that plant virus evolution to have low GC%genomes would have a unique function,which is to reduce the host AV-PTGS attack during infections.

关键词： anti-virus post-transcriptional gene silencing siRNA nucleotide bias Dicer-like Argonaute plant virus evolution

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Characterization of MicroRNA^＊ Species in Peking Duck Skin

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Journal of Integrative Agriculture 2013年第9期12卷 1614-1619页

作者： ZHANG Li XIE Xiu-juan JIA Shan-gang XIAO Mei LIN Shu-dai AN Li-long LUO Wen JIA Xin-zheng NIE Qing-hua ZHANG Xi-quan Agricultural College Guangdong Ocean University Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding South China Agricultural University Beijing Institute of Genomics Chinese Academy of Sciences

A substantial fraction of miRNA^＊ species are conserved in animals and can repress activities of target genes. This study aims to investigate the miRNA^＊ species in duck skin by using Solexa sequencing. We obtained a total of 96 miRNA^＊ species in two skin small RNA libraries and identified 56 miRNA/miRNA^＊（miR/miR^＊） pairs. nucleotide bias of miRNA^＊ indicated that the priority was C〉A〉U〉G for the first nucleotide and U〉C〉A〉G for the last nucleotide. Comparison analyses showed that 3＇-U accounted for a higher proportion in the 56 miR/miR＊ pairs. Among the top 20 expressed miRNA^＊ species, 17 were shared by two libraries and most of the miRNA^＊ species were highly conservative, especially in the ＂seed region＂, miR-199a^＊ were expressed highly in our samples, which was also previously shown abundant in mouse hair follicle. Furthermore, four miRNA^＊ species were predicted to target their genes in signal pathways of feather follicle development and feather morphogenesis despite very low levels.

关键词： Peking duck miRNA star species (miRNA&^*) skin nucleotide bias

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Analysis and Identification of miRNA Expression in the Skeletal Muscle of Sichuan White Rabbits

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Agricultural Biotechnology 2023年第3期12卷 66-69页

作者： Xiangyu ZHANG Kai ZHANG Bin WEN Dingsheng YUAN Chao YANG Yuying LI Liangde KUANG Rui YANG Congyan LI Jie ZHENG Yongjun REN Zhiqiang GUO Li TANG Yang JI Min LEI Dengping HUANG Xiaohong XIE Cuixia ZHANG Sichuan Animal Science Academy/Key Laboratory of animal genetics and breeding in Sichuan Province Chengdu 610066China Sichuan Academy of Grassland Sciences Chengdu 611743China

[Objectives]miRNAs play an important role in the proliferation and differentiation of different *** study was conducted to elucidate the complex genetic mechanisms that affect the meat production performance of Sichuan white rabbits and reveal the regulatory role of miRNAs in their muscle growth and meat quality formation.[Methods]Three constructed skeletal muscle libraries of Sichuan white rabbits aged six months were sequenced by the solexa technology to identify known miRNAs,predict new miRNAs and construct an expression profile of muscle miRNAs.[Results]A total of 511 known miRNAs and 42 miRNAs were detected in 34089472 pure sequences,and the proportion of miRNAs with a length of 22 nt was the *** number of known miRNA sequences accounted for 71.38%of pure sequences,which was much higher than the proportion of other types of *** proportion of sequences from exons was 0.38%,indicating a low degree of mRNA degradation in the *** U had the highest proportion at the first position,and the bases with the highest proportions at positions 8 and 10 were U and A,***-specific miRNAs(miR-1,miR-133,and miR-206)ranked in the top 10 in terms of expression *** number and expression levels of new miRNAs were lower than those of known *** length distribution,base bias at different positions and expression profile characteristics of miRNAs might be related to the biological function of miRNAs in regulating muscle proliferation and differentiation and the action mechanisms with target genes.[Conclusions]The identification and expression of miRNAs in muscle tissues of Sichuan white rabbits will help to understand the complex molecular mechanisms of meat production performance and provide a theoretical basis for the functional research of miRNAs in meat rabbits.

关键词： Meat rabbit Muscle High-throughput sequencing nucleotide bias

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