Yijun Meng

Summary

Affiliation: Zhejiang University
Country: China

Publications

  1. pmc Genome-wide identification of reverse complementary microRNA genes in plants
    Chaogang Shao
    College of Life Sciences, Huzhou Teachers College, Huzhou, The People s Republic of China
    PLoS ONE 7:e46991. 2012
  2. doi Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa)
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
    New Phytol 197:441-53. 2013
  3. pmc Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People s Republic of China
    PLoS ONE 7:e50870. 2012
  4. pmc Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Xiasha, Hangzhou 310036, PR China
    BMC Genomics 13:197. 2012
  5. doi Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
    RNA Biol 9:249-53. 2012
  6. pmc Large-scale identification of mirtrons in Arabidopsis and rice
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People s Republic of China
    PLoS ONE 7:e31163. 2012
  7. pmc RNA editing of nuclear transcripts in Arabidopsis thaliana
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, P R China
    BMC Genomics 11:S12. 2010
  8. doi Small RNAs in angiosperms: sequence characteristics, distribution and generation
    Dijun Chen
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences and James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, P R China
    Bioinformatics 26:1391-4. 2010
  9. doi MicroRNA-mediated signaling involved in plant root development
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    Biochem Biophys Res Commun 393:345-9. 2010
  10. pmc PmiRKB: a plant microRNA knowledge base
    Yijun Meng
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry and Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    Nucleic Acids Res 39:D181-7. 2011

Collaborators

Detail Information

Publications37

  1. pmc Genome-wide identification of reverse complementary microRNA genes in plants
    Chaogang Shao
    College of Life Sciences, Huzhou Teachers College, Huzhou, The People s Republic of China
    PLoS ONE 7:e46991. 2012
    ..Based on the results, we speculated that the mature RC-miRNAs might have subtle regulatory activity through target cleavages, but might possess short interfering RNA-like activity by guiding sequence-specific DNA methylation...
  2. doi Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa)
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
    New Phytol 197:441-53. 2013
    ..A set of rice stage-specific sRNAs along with the regulatory cascades, which have great potential in regulating specific developmental stages, were provided for further investigation...
  3. pmc Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People s Republic of China
    PLoS ONE 7:e50870. 2012
    ..Our bioinformatics survey expanded the organ-specific miRNA-target list in Arabidopsis, and could deepen the biological view of the miRNA expression and their regulatory roles...
  4. pmc Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Xiasha, Hangzhou 310036, PR China
    BMC Genomics 13:197. 2012
    ..Thus, limited evidences are available to provide detailed information for interrogating the questionable issue whether target mimicry was widespread in planta, and implicated in certain biological processes...
  5. doi Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
    RNA Biol 9:249-53. 2012
    ..We also hope to inspire further research efforts on the manual refinement of the current miRNA gene lists...
  6. pmc Large-scale identification of mirtrons in Arabidopsis and rice
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People s Republic of China
    PLoS ONE 7:e31163. 2012
    ..The result indicates that the mirtrons could guide target cleavages to exert their regulatory roles post-transcriptionally, which needs further experimental validation...
  7. pmc RNA editing of nuclear transcripts in Arabidopsis thaliana
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, P R China
    BMC Genomics 11:S12. 2010
    ..To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (Arabidopsis thaliana) was performed...
  8. doi Small RNAs in angiosperms: sequence characteristics, distribution and generation
    Dijun Chen
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences and James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, P R China
    Bioinformatics 26:1391-4. 2010
    ..One cis-NAT generates phased natural antisense short interfering RNAs (nat-siRNAs) specifically from flowers in Arabidopsis, while one in rice produces phased nat-siRNAs from grains, suggesting their organ-specific regulatory roles...
  9. doi MicroRNA-mediated signaling involved in plant root development
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    Biochem Biophys Res Commun 393:345-9. 2010
    ..Based on current research advances, several innovative mechanisms of miRNA transcription, feedback regulatory circuit between miRNAs and transcription factors (TFs), and miRNA-mediated signal interactions are also discussed...
  10. pmc PmiRKB: a plant microRNA knowledge base
    Yijun Meng
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry and Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    Nucleic Acids Res 39:D181-7. 2011
    ..PmiRKB can be freely accessed at http://bis.zju.edu.cn/pmirkb/...
  11. doi Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant
    Yijun Meng
    State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 310058 Hangzhou, People s Republic of China
    Planta 230:883-98. 2009
    ..Based on these findings, we also proposed a feedback circuit between miRNA(s) and ARF(s). The results presented here could serve as the basis for further in-depth studies of plant miRNAs involved in auxin signalling...
  12. pmc Plant siRNAs from introns mediate DNA methylation of host genes
    Dijun Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
    RNA 17:1012-24. 2011
    ..Finally, the 24-nt siRNAs incorporated with Argonaute 4 (AGO4) could direct DNA methylation on their host genes. In this regard, homeostatic self-regulation between intron-derived siRNAs and their host genes was proposed...
  13. doi Construction of microRNA- and microRNA*-mediated regulatory networks in plants
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
    RNA Biol 8:1124-48. 2011
    ..Further investigation of some specific subnetworks implied the utility of these networks for biologists. This study could broaden the current understanding of miRNA gene-mediated regulation in plants...
  14. doi Origin and evolutionary analysis of the plant-specific TIFY transcription factor family
    Youhuang Bai
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, PR China
    Genomics 98:128-36. 2011
    ..Evolutional analysis indicates that whole genome duplication and tandem duplication contributed to the expansion of the TIFY family in plants...
  15. doi Identification of the highly accumulated microRNA*s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)
    Chaogang Shao
    College of Life Sciences, Huzhou Teachers College, Huzhou 313000, PR China
    Gene 515:123-7. 2013
    ....
  16. doi Methodological framework for functional characterization of plant microRNAs
    Ming Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu hang tang Road 388, Hangzhou 310058, PR China
    J Exp Bot 61:2271-80. 2010
    ..However, numerous common methods are shared by these two miRNA research areas. Thus, this review will enhance our understanding of miRNA research methodology in organisms...
  17. doi High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism
    Yijun Meng
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    J Exp Bot 61:3833-7. 2010
    ..Here, the focus is on the recent research progress on this issue, and several interesting points were raised...
  18. doi Functional characterization of plant small RNAs based on next-generation sequencing data
    Ming Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
    Comput Biol Chem 34:308-12. 2010
    ..At last, we demonstrated that it was a great challenge for researchers to fully exploit these huge sRNA NGS datasets and numerous sRNA species remained to be uncovered and functionally characterized...
  19. doi Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis
    Chaogang Shao
    College of Life Sciences, Huzhou Teachers College, Huzhou 313000, PR China
    Gene 527:477-83. 2013
    ..1 and sRNA6-AT1G66310.1) were identified, providing a basis for in-depth functional analysis of these miRNA candidates. These results could update the current understanding of the biogenesis and the action of the plant miRNAs...
  20. pmc Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)
    Xiaoxia Ma
    College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16, Xiasha, Hangzhou 310036, PR China
    BMC Genomics 14:510. 2013
    ..However, whether the other small RNA (sRNA) species, which occupy a dominant portion of the plant endogenous sRNA population, possess potential roles in root development remains unclear...
  21. doi Toward microRNA-mediated gene regulatory networks in plants
    Yijun Meng
    Department of Bioinformatics and State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu hang tang Road 388, Hangzhou 310058, P R China
    Brief Bioinform 12:645-59. 2011
    ..It is desired that the introduced framework for miRNA-mediated network construction is timely and useful and could inspire more research efforts in the miRNA research area...
  22. pmc Mechanisms of microRNA-mediated auxin signaling inferred from the rice mutant osaxr
    Yijun Meng
    Department of Bioinformatics and State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
    Plant Signal Behav 5:252-4. 2010
    ....
  23. doi Epigenetic performers in plants
    Ming Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
    Dev Growth Differ 52:555-66. 2010
    ..Experimental technology to exploit these modifications, and proposed focus areas for future plant epigenetic research, are also presented...
  24. pmc PlantNATsDB: a comprehensive database of plant natural antisense transcripts
    Dijun Chen
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
    Nucleic Acids Res 40:D1187-93. 2012
    ..The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/...
  25. doi A reversed framework for the identification of microRNA-target pairs in plants
    Chaogang Shao
    College of Life Sciences, Huzhou Teachers College
    Brief Bioinform 14:293-301. 2013
    ..The results demonstrated the prevalent utility of the reversed approach for uncovering miRNA-target interactions in plants...
  26. pmc Long-range RNA pairings contribute to mutually exclusive splicing
    Yuan Yue
    Institute of Biochemistry, College of Life Sciences, Zhejiang University Zijingang Campus, Hangzhou, Zhejiang, ZJ310058, China
    RNA 22:96-110. 2016
    ..Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA-RNA interactions in gene regulatory networks. ..
  27. pmc miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining
    Lan Yu
    College of Life Sciences, Huzhou University, Huzhou 313000, P R China
    Sci Rep 6:18901. 2016
    ..Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html. ..
  28. pmc NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes
    Dongliang Yu
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
    Sci Rep 6:21666. 2016
    ..Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip...
  29. pmc Succinyl-proteome profiling of a high taxol containing hybrid Taxus species (Taxus × media) revealed involvement of succinylation in multiple metabolic pathways
    Chenjia Shen
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
    Sci Rep 6:21764. 2016
    ..These results provide the first comprehensive view of the succinylome of Taxus × media and may catalyze future biological investigation of succinylation...
  30. doi Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
    J Exp Bot 65:395-400. 2014
    ..Together, the results indicate that the proposed workflow is applicable for the identification of novel DCL1-dependent sRNA loci on plant genomes. ..
  31. doi CloneAssistant 1.0: a stand-alone software for automated cloning primer design
    Chaogang Shao
    College of Life Sciences, Huzhou University, Huzhou 313000, PR China
    J Biotechnol 150:294-8. 2010
    ..CloneAssistant 1.0" makes gene clone design much easier, and it can be freely downloaded from http://bis.zju.edu.cn/clone...
  32. pmc PRIN: a predicted rice interactome network
    Haibin Gu
    Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
    BMC Bioinformatics 12:161. 2011
    ..With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa...
  33. doi Is Argonaute 1 the only effective slicer of small RNA-mediated regulation of gene expression in plants?
    Chaogang Shao
    College of Life Sciences, Huzhou University, Huzhou 313000, PR China
    J Exp Bot 65:6293-9. 2014
    ..Based on the above results, the opinion was put forward that not only AGO1, but also AGO2, AGO5, AGO7, and AGO10 might be essential for the sRNA-mediated regulation of gene expression in plants. ..
  34. pmc An RNA architectural locus control region involved in Dscam mutually exclusive splicing
    Xuebin Wang
    Institute of Biochemistry, College of Life Sciences, Zhejiang University Zijingang Campus, Hangzhou, Zhejiang ZJ310058, China
    Nat Commun 3:1255. 2012
    ..Our findings not only provide a locus control region-dependent mechanism for mutually exclusive splicing, but also suggest a model for the evolution of increased complexity in a long-range RNA molecular machine...
  35. doi The function of LPR1 is controlled by an element in the promoter and is independent of SUMO E3 Ligase SIZ1 in response to low Pi stress in Arabidopsis thaliana
    Xuemin Wang
    State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, PR China
    Plant Cell Physiol 51:380-94. 2010
    ..The insensitive response of the psi mutant to brefeldin A suggests that LPR1 and PDR2 (Pi Deficiency Response 2) function in opposite ways in regulating the root growth response to Pi starvation in the endoplamic reticulum...
  36. pmc A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb
    Yijun Meng
    College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
    Sci Rep 6:18864. 2016
    ..ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb. ..
  37. doi Are ta-siRNAs only originated from the cleavage site of miRNA on its target RNAs and phased in 21-nt increments?
    Lan Yu
    College of Life Sciences, Huzhou University, Huzhou 313000, PR China
    Gene 569:127-35. 2015
    ..Based on these results, we propose that the canonical biogenesis model of ta-siRNAs should be modified in order to recruit the previously unidentified ta-siRNA candidates...