메뉴 건너뛰기




Volumn 9, Issue 2, 2014, Pages

A contig-based strategy for the genome-wide discovery of MicroRNAs without complete genome resources

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MICRORNA; SHORT HAIRPIN RNA;

EID: 84895747688     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088179     Document Type: Article
Times cited : (11)

References (45)
  • 1
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 2
    • 0038299558 scopus 로고    scopus 로고
    • Role of microRNAs in plant and animal development
    • DOI 10.1126/science.1085242
    • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338. (Pubitemid 36877060)
    • (2003) Science , vol.301 , Issue.5631 , pp. 336-338
    • Carrington, J.C.1    Ambros, V.2
  • 3
    • 60149086351 scopus 로고    scopus 로고
    • Origin, Biogenesis, and Activity of Plant MicroRNAs
    • Voinnet O (2009) Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell 136: 669-687.
    • (2009) Cell , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 4
    • 34347355440 scopus 로고    scopus 로고
    • miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • DOI 10.1038/nature05903, PII NATURE05903
    • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447: 1126-1129. (Pubitemid 47014429)
    • (2007) Nature , vol.447 , Issue.7148 , pp. 1126-1129
    • Molnar, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 5
    • 34249093687 scopus 로고    scopus 로고
    • A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
    • Zhao T, Li G, Mi S, Li S, Hannon GJ, et al. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 21: 1190-1203.
    • (2007) Genes Dev , vol.21 , pp. 1190-1203
    • Zhao, T.1    Li, G.2    Mi, S.3    Li, S.4    Hannon, G.J.5
  • 8
    • 77953217767 scopus 로고    scopus 로고
    • Arabidopsis lyrata Small RNAs: Transient MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus
    • Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata Small RNAs: Transient MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus. Plant Cell 22: 1090-1103.
    • (2010) Plant Cell , vol.22 , pp. 1090-1103
    • Ma, Z.1    Coruh, C.2    Axtell, M.J.3
  • 9
    • 33847311819 scopus 로고    scopus 로고
    • MicroRNAs and Immunity: Tiny Players in a Big Field
    • DOI 10.1016/j.immuni.2007.02.005, PII S1074761307001446
    • Taganov KD, Boldin MP, Baltimore D (2007) MicroRNAs and immunity: tiny players in a big field. Immunity 26: 133-137. (Pubitemid 46329443)
    • (2007) Immunity , vol.26 , Issue.2 , pp. 133-137
    • Taganov, K.D.1    Boldin, M.P.2    Baltimore, D.3
  • 10
    • 68749100821 scopus 로고    scopus 로고
    • The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis
    • Wu G, Park MY, Conway SR, Wang JW, Weigel D, et al. (2009) The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis. Cell 138: 750-759.
    • (2009) Cell , vol.138 , pp. 750-759
    • Wu, G.1    Park, M.Y.2    Conway, S.R.3    Wang, J.W.4    Weigel, D.5
  • 11
    • 33748769519 scopus 로고    scopus 로고
    • Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice
    • DOI 10.1104/pp.106.084475
    • Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiology 142: 280-293. (Pubitemid 44412247)
    • (2006) Plant Physiology , vol.142 , Issue.1 , pp. 280-293
    • Xie, K.1    Wu, C.2    Xiong, L.3
  • 13
    • 50649110065 scopus 로고    scopus 로고
    • A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    • Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, et al. (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research 18: 1456-1465.
    • (2008) Genome Research , vol.18 , pp. 1456-1465
    • Zhu, Q.H.1    Spriggs, A.2    Matthew, L.3    Fan, L.4    Kennedy, G.5
  • 14
    • 34848898946 scopus 로고    scopus 로고
    • Conservation and evolution of miRNA regulatory programs in plant development
    • DOI 10.1016/j.pbi.2007.07.004, PII S1369526607000866, Cell Signalling and Gene Regulation Edited by Jian-Kang Zhu and Ko Shimamoto
    • Willmann MR, Poethig RS (2007) Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 10: 503-511. (Pubitemid 47503879)
    • (2007) Current Opinion in Plant Biology , vol.10 , Issue.5 , pp. 503-511
    • Willmann, M.R.1    Poethig, R.S.2
  • 17
    • 80052792180 scopus 로고    scopus 로고
    • mirExplorer: Detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features
    • Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH (2011) mirExplorer: detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features. RNA Biol 8: 922-934.
    • (2011) RNA Biol , vol.8 , pp. 922-934
    • Guan, D.G.1    Liao, J.Y.2    Qu, Z.H.3    Zhang, Y.4    Qu, L.H.5
  • 18
    • 33646830110 scopus 로고    scopus 로고
    • Conservation and divergence of plant microRNA genes
    • DOI 10.1111/j.1365-313X.2006.02697.x
    • Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259. (Pubitemid 43773564)
    • (2006) Plant Journal , vol.46 , Issue.2 , pp. 243-259
    • Zhang, B.1    Pan, X.2    Cannon, C.H.3    Cobb, G.P.4    Anderson, T.A.5
  • 19
    • 39549115890 scopus 로고    scopus 로고
    • Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)
    • Yao Y, Guo G, Ni Z, Sunkar R, Du J, et al. (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8: R96.
    • (2007) Genome Biol , vol.8
    • Yao, Y.1    Guo, G.2    Ni, Z.3    Sunkar, R.4    Du, J.5
  • 20
    • 81155134417 scopus 로고    scopus 로고
    • Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by highthroughput sequencing
    • Chi X, Yang Q, Chen X, Wang J, Pan L, et al. (2011) Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by highthroughput sequencing. PloS One 6: e27530.
    • (2011) PloS One , vol.6
    • Chi, X.1    Yang, Q.2    Chen, X.3    Wang, J.4    Pan, L.5
  • 21
    • 84861338860 scopus 로고    scopus 로고
    • Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
    • Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, et al. (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13: 83.
    • (2012) BMC Genomics , vol.13 , pp. 83
    • Pelaez, P.1    Trejo, M.S.2    Iniguez, L.P.3    Estrada-Navarrete, G.4    Covarrubias, A.A.5
  • 22
    • 84858980069 scopus 로고    scopus 로고
    • Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics
    • Wang C, Han J, Liu C, Kibet KN, Kayesh E, et al. (2012) Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 13: 122.
    • (2012) BMC Genomics , vol.13 , pp. 122
    • Wang, C.1    Han, J.2    Liu, C.3    Kibet, K.N.4    Kayesh, E.5
  • 23
    • 84864828309 scopus 로고    scopus 로고
    • High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp pekinensis)
    • Wang F, Li L, Liu L, Li H, Zhang Y, et al. (2012) High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp pekinensis). Molecular Genetics and Genomics 287: 555-563.
    • (2012) Molecular Genetics and Genomics , vol.287 , pp. 555-563
    • Wang, F.1    Li, L.2    Liu, L.3    Li, H.4    Zhang, Y.5
  • 24
    • 84865131821 scopus 로고    scopus 로고
    • In-silico and invivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus
    • Catalano D, Pignone D, Sonnante G, Finetti-Sialer MM (2012) In-silico and invivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. BMC Bioinformatics 13.
    • (2012) BMC Bioinformatics , vol.13
    • Catalano, D.1    Pignone, D.2    Sonnante, G.3    Finetti-Sialer, M.M.4
  • 25
    • 84861872022 scopus 로고    scopus 로고
    • Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets
    • Gebelin V, Argout X, Engchuan W, Pitollat B, Duan CF, et al. (2012) Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. BMC Plant Biology 12.
    • (2012) BMC Plant Biology , vol.12
    • Gebelin, V.1    Argout, X.2    Engchuan, W.3    Pitollat, B.4    Duan, C.F.5
  • 26
    • 77955387859 scopus 로고    scopus 로고
    • Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags
    • Song C, Jia Q, Fang J, Li F, Wang C, et al. (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biology 12: 927-934.
    • (2010) Plant Biology , vol.12 , pp. 927-934
    • Song, C.1    Jia, Q.2    Fang, J.3    Li, F.4    Wang, C.5
  • 27
    • 0042232552 scopus 로고    scopus 로고
    • Expressed sequence tags: Alternative or complement to whole genome sequences?
    • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8: 321-329.
    • (2003) Trends in Plant Science , vol.8 , pp. 321-329
    • Rudd, S.1
  • 28
    • 19944384237 scopus 로고    scopus 로고
    • Comparative EST analyses in plant systems
    • DOI 10.1016/S0076-6879(05)95022-2, PII S0076687905950222, Molecular Evolution: Producing the Biochemical Data
    • Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V (2005) Comparative EST analyses in plant systems. Methods in Enzymology 395: 400-418. (Pubitemid 40754379)
    • (2005) Methods in Enzymology , vol.395 , pp. 400-418
    • Dong, Q.1    Kroiss, L.2    Oakley, F.D.3    Wang, B.-B.4    Brendel, V.5
  • 29
    • 51849142774 scopus 로고    scopus 로고
    • The Silkworm (Bombyx mori) microRNAs and Their Expressions in Multiple Developmental Stages
    • Yu XM, Zhou Q, Li SC, Luo QB, Cai YM, et al. (2008) The Silkworm (Bombyx mori) microRNAs and Their Expressions in Multiple Developmental Stages. PloS One 3.
    • (2008) PloS One , vol.3
    • Yu, X.M.1    Zhou, Q.2    Li, S.C.3    Luo, Q.B.4    Cai, Y.M.5
  • 30
    • 84864696893 scopus 로고    scopus 로고
    • The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
    • D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213-217.
    • (2012) Nature , vol.488 , pp. 213-217
    • D'Hont, A.1    Denoeud, F.2    Aury, J.M.3    Baurens, F.C.4    Carreel, F.5
  • 32
    • 84865304222 scopus 로고    scopus 로고
    • Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis
    • Xu MY, Dong Y, Zhang QX, Zhang L, Luo YZ, et al. (2012) Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics 13.
    • (2012) BMC Genomics , vol.13
    • Xu, M.Y.1    Dong, Y.2    Zhang, Q.X.3    Zhang, L.4    Luo, Y.Z.5
  • 33
    • 84859495972 scopus 로고    scopus 로고
    • Identification and Characterization of MicroRNAs in Asiatic Cotton (Gossypium arboreum L.)
    • Wang M, Wang Q, Wang B (2012) Identification and Characterization of MicroRNAs in Asiatic Cotton (Gossypium arboreum L.). PloS One 7.
    • (2012) PloS One , vol.7
    • Wang, M.1    Wang, Q.2    Wang, B.3
  • 34
    • 27844495281 scopus 로고    scopus 로고
    • Identification and characterization of new plant microRNAs using EST analysis
    • DOI 10.1038/sj.cr.7290302
    • Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15: 336-360. (Pubitemid 41653929)
    • (2005) Cell Research , vol.15 , Issue.5 , pp. 336-360
    • Zhang, B.H.1    Pan, X.P.2    Wang, Q.L.3    Cobb, G.P.4    Anderson, T.A.5
  • 35
    • 7644237777 scopus 로고    scopus 로고
    • Intron-derived microRNAs-fine tuning of gene functions
    • Ying SY, Lin SL (2004) Intron-derived microRNAs-fine tuning of gene functions. Gene 342: 25-28.
    • (2004) Gene , vol.342 , pp. 25-28
    • Ying, S.Y.1    Lin, S.L.2
  • 37
    • 0036021693 scopus 로고    scopus 로고
    • Mechanisms and rates of genome expansion and contraction in flowering plants
    • Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36.
    • (2002) Genetica , vol.115 , pp. 29-36
    • Bennetzen, J.L.1
  • 38
    • 33846474760 scopus 로고    scopus 로고
    • A hitchhiker's guide to expressed sequence tag (EST) analysis
    • DOI 10.1093/bib/bbl015
    • Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics 8: 6-21. (Pubitemid 46157926)
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.1 , pp. 6-21
    • Nagaraj, S.H.1    Gasser, R.B.2    Ranganathan, S.3
  • 39
    • 78651307694 scopus 로고    scopus 로고
    • starBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
    • Yang JH, Li JH, Shao P, Zhou H, Chen YQ, et al. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39: D202-209.
    • (2011) Nucleic Acids Res , vol.39
    • Yang, J.H.1    Li, J.H.2    Shao, P.3    Zhou, H.4    Chen, Y.Q.5
  • 40
    • 84884152199 scopus 로고    scopus 로고
    • Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching
    • Zhang YC, Yu Y, Wang CY, Li ZY, Liu Q, et al. (2013) Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nat Biotechnol 31: 848-852.
    • (2013) Nat Biotechnol , vol.31 , pp. 848-852
    • Zhang, Y.C.1    Yu, Y.2    Wang, C.Y.3    Li, Z.Y.4    Liu, Q.5
  • 41
    • 84862986116 scopus 로고    scopus 로고
    • Phylogeny: Rewriting evolution
    • Dolgin E (2012) Phylogeny: Rewriting evolution. Nature 486: 460-462.
    • (2012) Nature , vol.486 , pp. 460-462
    • Dolgin, E.1
  • 42
    • 79957741638 scopus 로고    scopus 로고
    • Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei
    • Wen YZ, Zheng LL, Liao JY, Wang MH, Wei Y, et al. (2011) Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proc Natl Acad Sci U S A 108: 8345-8350.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 8345-8350
    • Wen, Y.Z.1    Zheng, L.L.2    Liao, J.Y.3    Wang, M.H.4    Wei, Y.5
  • 43
    • 84879303464 scopus 로고    scopus 로고
    • Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei
    • Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, et al. (2013) Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA 19: 863-875.
    • (2013) RNA , vol.19 , pp. 863-875
    • Zheng, L.L.1    Wen, Y.Z.2    Yang, J.H.3    Liao, J.Y.4    Shao, P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.