메뉴 건너뛰기




Volumn 13, Issue 1, 2015, Pages

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs

Author keywords

Evolution; Function; Plant phasiRNAs; Protein coding genes

Indexed keywords

ALGAE; BRYOPHYTA; DICOTYLEDONEAE; GYMNOSPERMAE; MAGNOLIOPHYTA;

EID: 85019203917     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-015-0142-4     Document Type: Article
Times cited : (54)

References (67)
  • 1
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNAs
    • Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell. 2009;136:669-87. doi: 10.1016/j.cell.2009.01.046 .
    • (2009) Cell. , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 2
    • 79955111192 scopus 로고    scopus 로고
    • Small RNA-mediated epigenetic modifications in plants
    • Simon SA, Meyers BC. Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol. 2011;14:148-55. doi: 10.1016/j.pbi.2010.11.007 .
    • (2011) Curr Opin Plant Biol. , vol.14 , pp. 148-155
    • Simon, S.A.1    Meyers, B.C.2
  • 3
    • 84881501607 scopus 로고    scopus 로고
    • miRNA biogenesis and turnover in plants
    • Rogers K, Chen X. miRNA biogenesis and turnover in plants. Cold Spring Harb Symp Quant Biol. 2012;77:183-94. doi: 10.1101/sqb.2013.77.014530 .
    • (2012) Cold Spring Harb Symp Quant Biol , vol.77 , pp. 183-194
    • Rogers, K.1    Chen, X.2
  • 4
    • 79955379930 scopus 로고    scopus 로고
    • Vive la difference: biogenesis and evolution of microRNAs in plants and animals
    • Axtell MJ, Westholm JO, Lai EC. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 2011;12:221. doi: 10.1186/gb-2011-12-4-221 .
    • (2011) Genome Biol. , vol.12 , pp. 221
    • Axtell, M.J.1    Westholm, J.O.2    Lai, E.C.3
  • 5
    • 81355123438 scopus 로고    scopus 로고
    • Evolution of microRNA diversity and regulation in animals
    • Berezikov E. Evolution of microRNA diversity and regulation in animals. Nat Rev Genet. 2011;12:846-60. doi: 10.1038/nrg3079 .
    • (2011) Nat Rev Genet. , vol.12 , pp. 846-860
    • Berezikov, E.1
  • 6
    • 79953086307 scopus 로고    scopus 로고
    • Evolution and functional diversification of MIRNA genes
    • Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell. 2011;23:431-42. doi: 10.1105/tpc.110.082784 .
    • (2011) Plant Cell. , vol.23 , pp. 431-442
    • Cuperus, J.T.1    Fahlgren, N.2    Carrington, J.C.3
  • 7
    • 84883166485 scopus 로고    scopus 로고
    • Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks
    • Fei Q, Xia R, Meyers BC. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell. 2013;25:2400-15. doi: 10.1105/tpc.113.114652 .
    • (2013) Plant Cell. , vol.25 , pp. 2400-2415
    • Fei, Q.1    Xia, R.2    Meyers, B.C.3
  • 8
    • 84877677064 scopus 로고    scopus 로고
    • Classification and comparison of small RNAs from plants
    • Axtell MJ. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol. 2013;64:137-59. doi: 10.1146/annurev-arplant-050312-120043 .
    • (2013) Annu Rev Plant Biol. , vol.64 , pp. 137-159
    • Axtell, M.J.1
  • 9
    • 4644286235 scopus 로고    scopus 로고
    • SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis
    • Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 2004;18:2368-79. doi: 10.1101/gad.1231804 .
    • (2004) Genes Dev. , vol.18 , pp. 2368-2379
    • Peragine, A.1    Yoshikawa, M.2    Wu, G.3    Albrecht, H.L.4    Poethig, R.S.5
  • 10
    • 4944225347 scopus 로고    scopus 로고
    • Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs
    • Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell. 2004;16:69-79. doi: 10.1016/j.molcel.2004.09.028 .
    • (2004) Mol Cell. , vol.16 , pp. 69-79
    • Vazquez, F.1    Vaucheret, H.2    Rajagopalan, R.3    Lepers, C.4    Gasciolli, V.5    Mallory, A.C.6
  • 11
    • 17444430392 scopus 로고    scopus 로고
    • microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    • Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005;121:207-21. doi: 10.1016/j.cell.2005.04.004 .
    • (2005) Cell , vol.121 , pp. 207-221
    • Allen, E.1    Xie, Z.2    Gustafson, A.M.3    Carrington, J.C.4
  • 12
    • 33750440526 scopus 로고    scopus 로고
    • A two-hit trigger for siRNA biogenesis in plants
    • Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants. Cell. 2006;127:565-77. doi: 10.1016/j.cell.2006.09.032 .
    • (2006) Cell. , vol.127 , pp. 565-577
    • Axtell, M.J.1    Jan, C.2    Rajagopalan, R.3    Bartel, D.P.4
  • 13
    • 84873033996 scopus 로고    scopus 로고
    • miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens
    • Cho SH, Coruh C, Axtell MJ. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens. Plant Cell. 2012;24:4837-49. doi: 10.1105/tpc.112.103176 .
    • (2012) Plant Cell , vol.24 , pp. 4837-4849
    • Cho, S.H.1    Coruh, C.2    Axtell, M.J.3
  • 14
    • 84919664945 scopus 로고    scopus 로고
    • Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development
    • Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M, Timmermans MC. Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development. PLoS Genet. 2014;10:e1004826. doi: 10.1371/journal.pgen.1004826 .
    • (2014) PLoS Genet. , vol.10 , pp. e1004826
    • Dotto, M.C.1    Petsch, K.A.2    Aukerman, M.J.3    Beatty, M.4    Hammell, M.5    Timmermans, M.C.6
  • 15
    • 82955207556 scopus 로고    scopus 로고
    • microRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
    • Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, et al. microRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev. 2011;25:2540-53. doi: 10.1101/gad.177527.111 .
    • (2011) Genes Dev , vol.25 , pp. 2540-2553
    • Zhai, J.1    Jeong, D.H.2    Paoli, E.3    Park, S.4    Rosen, B.D.5    Li, Y.6
  • 16
    • 84961288187 scopus 로고    scopus 로고
    • An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes
    • Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, et al. An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. Plant Cell. 2014;26:4584-601. doi: 10.1105/tpc.114.131847 .
    • (2014) Plant Cell. , vol.26 , pp. 4584-4601
    • Arikit, S.1    Xia, R.2    Kakrana, A.3    Huang, K.4    Zhai, J.5    Yan, Z.6
  • 18
    • 84860126087 scopus 로고    scopus 로고
    • A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs
    • Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell. 2012;24:859-74. doi: 10.1105/tpc.111.095380 .
    • (2012) Plant Cell. , vol.24 , pp. 859-874
    • Shivaprasad, P.V.1    Chen, H.M.2    Patel, K.3    Bond, D.M.4    Santos, B.A.5    Baulcombe, D.C.6
  • 19
    • 84893780640 scopus 로고    scopus 로고
    • The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes
    • Boccara M, Sarazin A, Thiebeauld O, Jay F, Voinnet O, Navarro L, et al. The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes. PLoS Pathog. 2014;10:e1003883. doi: 10.1371/journal.ppat.1003883 .
    • (2014) PLoS Pathog. , vol.10 , pp. e1003883
    • Boccara, M.1    Sarazin, A.2    Thiebeauld, O.3    Jay, F.4    Voinnet, O.5    Navarro, L.6
  • 20
    • 84862232060 scopus 로고    scopus 로고
    • Apple miRNAs and tasiRNAs with novel regulatory networks
    • Xia R, Zhu H, An YQ, Beers EP, Liu Z. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol. 2012;13:R47. doi: 10.1186/gb-2012-13-6-r47 .
    • (2012) Genome Biol. , vol.13 , pp. R47
    • Xia, R.1    Zhu, H.2    An, Y.Q.3    Beers, E.P.4    Liu, Z.5
  • 21
    • 84865097020 scopus 로고    scopus 로고
    • Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs
    • Zhu H, Xia R, Zhao B, An YQ, Dardick CD, Callahan AM, et al. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol. 2012;12:149. doi: 10.1186/1471-2229-12-149 .
    • (2012) BMC Plant Biol. , vol.12 , pp. 149
    • Zhu, H.1    Xia, R.2    Zhao, B.3    An, Y.Q.4    Dardick, C.D.5    Callahan, A.M.6
  • 22
    • 34250717043 scopus 로고    scopus 로고
    • Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
    • Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell. 2007;19:926-42. doi: 10.1105/tpc.107 .
    • (2007) Plant Cell. , vol.19 , pp. 926-942
    • Howell, M.D.1    Fahlgren, N.2    Chapman, E.J.3    Cumbie, J.S.4    Sullivan, C.M.5    Givan, S.A.6
  • 23
    • 84879466274 scopus 로고    scopus 로고
    • microRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots
    • Xia R, Meyers BC, Liu Z, Beers EP, Ye S, Liu Z. microRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. Plant Cell. 2013;25:1555-72. doi: 10.1105/tpc.113.110957 .
    • (2013) Plant Cell , vol.25 , pp. 1555-1572
    • Xia, R.1    Meyers, B.C.2    Liu, Z.3    Beers, E.P.4    Ye, S.5    Liu, Z.6
  • 24
    • 33847652140 scopus 로고    scopus 로고
    • Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis
    • Chen HM, Li YH, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci U S A. 2007;104:3318-23. doi: 10.1073/pnas.0611119104 .
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 3318-3323
    • Chen, H.M.1    Li, Y.H.2    Wu, S.H.3
  • 25
    • 80053583176 scopus 로고    scopus 로고
    • miR393 and secondary siRNAs regulate expression of the TIR1/AFB2 auxin receptor clade and auxin-related development of Arabidopsis leaves
    • Si-Ammour A, Windels D, Arn-bouldoires E, Kutter C, Ailhas J, Meins F, et al. miR393 and secondary siRNAs regulate expression of the TIR1/AFB2 auxin receptor clade and auxin-related development of Arabidopsis leaves. Plant Physiol. 2011;157:683-91. doi: 10.1104/pp.111.180083 .
    • (2011) Plant Physiol , vol.157 , pp. 683-691
    • Si-Ammour, A.1    Windels, D.2    Arn-bouldoires, E.3    Kutter, C.4    Ailhas, J.5    Meins, F.6
  • 26
    • 80055000264 scopus 로고    scopus 로고
    • Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth
    • Wang Y, Itaya A, Zhong X, Wu Y, Zhang J, van der Knaap E, et al. Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell. 2011;23:3185-203. doi: 10.1105/tpc.111.088013 .
    • (2011) Plant Cell. , vol.23 , pp. 3185-3203
    • Wang, Y.1    Itaya, A.2    Zhong, X.3    Wu, Y.4    Zhang, J.5    Knaap, E.6
  • 27
    • 34547668337 scopus 로고    scopus 로고
    • Common functions for diverse small RNAs of land plants
    • Axtell MJ, Snyder JA, Bartel DP. Common functions for diverse small RNAs of land plants. Plant Cell. 2007;19:1750-69. doi: 10.1105/tpc.107.051706 .
    • (2007) Plant Cell. , vol.19 , pp. 1750-1769
    • Axtell, M.J.1    Snyder, J.A.2    Bartel, D.P.3
  • 29
    • 77950367420 scopus 로고    scopus 로고
    • Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection
    • Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan EM, Fahlgren N, Brempelis KJ, et al. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection. Plant Cell. 2010;22:481-96. doi: 10.1105/tpc.109.073056 .
    • (2010) Plant Cell. , vol.22 , pp. 481-496
    • Garcia-Ruiz, H.1    Takeda, A.2    Chapman, E.J.3    Sullivan, E.M.4    Fahlgren, N.5    Brempelis, K.J.6
  • 30
    • 77950346035 scopus 로고    scopus 로고
    • Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
    • He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 2010;22:17-33. doi: 10.1105/tpc.109.072041 .
    • (2010) Plant Cell. , vol.22 , pp. 17-33
    • He, G.1    Zhu, X.2    Elling, A.A.3    Chen, L.4    Wang, X.5    Guo, L.6
  • 31
    • 80052339278 scopus 로고    scopus 로고
    • Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors
    • Du P, Wu J, Zhang J, Zhao S, Zheng H, Gao G, et al. Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog. 2011;7:e1002176. doi: 10.1371/journal.ppat.1002176 .
    • (2011) PLoS Pathog. , vol.7 , pp. e1002176
    • Du, P.1    Wu, J.2    Zhang, J.3    Zhao, S.4    Zheng, H.5    Gao, G.6
  • 32
    • 84867402407 scopus 로고    scopus 로고
    • Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication
    • Wang Y, Bai X, Yan C, Gui Y, Wei X, Zhu QH, et al. Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication. New Phytol. 2012;196:914-25. doi: 10.1111/j.1469-8137.2012.04304.x .
    • (2012) New Phytol. , vol.196 , pp. 914-925
    • Wang, Y.1    Bai, X.2    Yan, C.3    Gui, Y.4    Wei, X.5    Zhu, Q.H.6
  • 33
    • 84899487011 scopus 로고    scopus 로고
    • Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs
    • Montes RA, de Fatima R-CF, De Paoli E, Accerbi M, Rymarquis LA, Mahalingam G, et al. Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun. 2014;5:3722. doi: 10.1038/ncomms4722 .
    • (2014) Nat Commun. , vol.5 , pp. 3722
    • Montes, R.A.1    Fatima, R.-C.F.2    Paoli, E.3    Accerbi, M.4    Rymarquis, L.A.5    Mahalingam, G.6
  • 34
    • 84930647139 scopus 로고    scopus 로고
    • Plant Phased Secondary siRNA Database. [ http://bioinfo.bti.cornell.edu/tool/phasiRNA ].
  • 35
    • 84887025720 scopus 로고    scopus 로고
    • Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development?
    • Rock CD. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends Plant Sci. 2013;18:601-10. doi: 10.1016/j.tplants.2013.07.006 .
    • (2013) Trends Plant Sci. , vol.18 , pp. 601-610
    • Rock, C.D.1
  • 36
    • 84892773410 scopus 로고    scopus 로고
    • miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development
    • Guan X, Pang M, Nah G, Shi X, Ye W, Stelly DM, et al. miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nat Commun. 2014;5:3050. doi: 10.1038/ncomms4050 .
    • (2014) Nat Commun , vol.5 , pp. 3050
    • Guan, X.1    Pang, M.2    Nah, G.3    Shi, X.4    Ye, W.5    Stelly, D.M.6
  • 37
    • 84865425907 scopus 로고    scopus 로고
    • An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis
    • Luo QJ, Mittal A, Jia F, Rock CD. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol. 2012;80:117-29. doi: 10.1007/s11103-011-9778-9 .
    • (2012) Plant Mol Biol. , vol.80 , pp. 117-129
    • Luo, Q.J.1    Mittal, A.2    Jia, F.3    Rock, C.D.4
  • 38
    • 84855481496 scopus 로고    scopus 로고
    • Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits
    • Zuo J, Zhu B, Fu D, Zhu Y, Ma Y, Chi L, et al. Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. BMC Genomics. 2012;13:7. doi: 10.1186/1471-2164-13-7 .
    • (2012) BMC Genomics. , vol.13 , pp. 7
    • Zuo, J.1    Zhu, B.2    Fu, D.3    Zhu, Y.4    Ma, Y.5    Chi, L.6
  • 39
    • 0037653656 scopus 로고    scopus 로고
    • Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana
    • Tian D, Traw MB, Chen JQ, Kreitman M, Bergelson J. Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature. 2003;423:74-7. doi: 10.1038/nature01588 .
    • (2003) Nature. , vol.423 , pp. 74-77
    • Tian, D.1    Traw, M.B.2    Chen, J.Q.3    Kreitman, M.4    Bergelson, J.5
  • 40
    • 24944491201 scopus 로고    scopus 로고
    • A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis
    • Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 2005;19:2164-75. doi: 10.1101/gad.1352605 .
    • (2005) Genes Dev. , vol.19 , pp. 2164-2175
    • Yoshikawa, M.1    Peragine, A.2    Park, M.Y.3    Poethig, R.S.4
  • 41
    • 84930623701 scopus 로고    scopus 로고
    • Phytozome. [ http://www.phytozome.net ].
  • 42
    • 84930670840 scopus 로고    scopus 로고
    • Sol Genomics Network. [ http://solgenomics.net ].
  • 43
    • 84930683286 scopus 로고    scopus 로고
    • Amborella Genome Database. [ http://www.amborella.org ].
  • 44
    • 84873587727 scopus 로고    scopus 로고
    • Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
    • Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013;31:154-9. doi: 10.1038/nbt.2462 .
    • (2013) Nat Biotechnol. , vol.31 , pp. 154-159
    • Zhong, S.1    Fei, Z.2    Chen, Y.R.3    Zheng, Y.4    Huang, M.5    Vrebalov, J.6
  • 45
    • 84924308731 scopus 로고    scopus 로고
    • Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers
    • Zhai J, Zhang H, Arikit S, Huang K, Nan GL, Walbot V, et al. Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci U S A. 2015;112:3146-51. doi: 10.1073/pnas.1418918112 .
    • (2015) Proc Natl Acad Sci U S A. , vol.112 , pp. 3146-3151
    • Zhai, J.1    Zhang, H.2    Arikit, S.3    Huang, K.4    Nan, G.L.5    Walbot, V.6
  • 46
    • 45549091152 scopus 로고    scopus 로고
    • Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection
    • Babu M, Gagarinova AG, Brandle JE, Wang A. Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection. J Gen Virol. 2008;89:1069-80. doi: 10.1099/vir.0.83531-0 .
    • (2008) J Gen Virol. , vol.89 , pp. 1069-1080
    • Babu, M.1    Gagarinova, A.G.2    Brandle, J.E.3    Wang, A.4
  • 47
    • 72949087809 scopus 로고    scopus 로고
    • Comparative analysis of expression profiles in shoots and roots of tomato systemically infected by Tomato spotted wilt virus reveals organ-specific transcriptional responses
    • Catoni M, Miozzi L, Fiorilli V, Lanfranco L, Accotto GP. Comparative analysis of expression profiles in shoots and roots of tomato systemically infected by Tomato spotted wilt virus reveals organ-specific transcriptional responses. Mol Plant Microbe Interact. 2009;22:1504-13. doi: 10.1094/MPMI-22-12-1504 .
    • (2009) Mol Plant Microbe Interact. , vol.22 , pp. 1504-1513
    • Catoni, M.1    Miozzi, L.2    Fiorilli, V.3    Lanfranco, L.4    Accotto, G.P.5
  • 48
    • 79956003318 scopus 로고    scopus 로고
    • Differential tomato transcriptomic responses induced by Pepino mosaic virus isolates with differential aggressiveness
    • Hanssen IM, van Esse HP, Ballester AR, Hogewoning SW, Parra NO, Paeleman A, et al. Differential tomato transcriptomic responses induced by Pepino mosaic virus isolates with differential aggressiveness. Plant Physiol. 2011;156:301-18. doi: 10.1104/pp. 111.173906 .
    • (2011) Plant Physiol. , vol.156 , pp. 301-318
    • Hanssen, I.M.1    Esse, H.P.2    Ballester, A.R.3    Hogewoning, S.W.4    Parra, N.O.5    Paeleman, A.6
  • 49
    • 84865515446 scopus 로고    scopus 로고
    • Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development
    • Lu J, Du ZX, Kong J, Chen LN, Qiu YH, Li GF, et al. Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development. PLoS One. 2012;7:e43447. doi: 10.1371/journal.pone.0043447 .
    • (2012) PLoS One. , vol.7 , pp. e43447
    • Lu, J.1    Du, Z.X.2    Kong, J.3    Chen, L.N.4    Qiu, Y.H.5    Li, G.F.6
  • 50
    • 84894073264 scopus 로고    scopus 로고
    • Comparative transcriptome profiling of a resistant vs. susceptible tomato (Solanum lycopersicum) cultivar in response to infection by Tomato yellow leaf curl virus
    • Chen T, Lv Y, Zhao T, Li N, Yang Y, Yu W, et al. Comparative transcriptome profiling of a resistant vs. susceptible tomato (Solanum lycopersicum) cultivar in response to infection by Tomato yellow leaf curl virus. PLoS One. 2013;8:e80816. doi: 10.1371/journal.pone.0080816 .
    • (2013) PLoS One. , vol.8 , pp. e80816
    • Chen, T.1    Lv, Y.2    Zhao, T.3    Li, N.4    Yang, Y.5    Yu, W.6
  • 51
    • 34347355440 scopus 로고    scopus 로고
    • miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature. 2007;447:1126-9. doi: 10.1038/nature05903 .
    • (2007) Nature , vol.447 , pp. 1126-1129
    • Molnar, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 52
    • 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, Wang XJ, et al. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev. 2007;21:1190-203. doi: 10.1101/gad.1543507 .
    • (2007) Genes Dev. , vol.21 , pp. 1190-1203
    • Zhao, T.1    Li, G.2    Mi, S.3    Li, S.4    Hannon, G.J.5    Wang, X.J.6
  • 53
    • 52049104255 scopus 로고    scopus 로고
    • Diversification of the core RNA interference machinery in Chlamydomonas reinhardtii and the role of DCL1 in transposon silencing
    • Casas-Mollano JA, Rohr J, Kim EJ, Balassa E, van Dijk K, Cerutti H. Diversification of the core RNA interference machinery in Chlamydomonas reinhardtii and the role of DCL1 in transposon silencing. Genetics. 2008;179:69-81. doi: 10.1534/genetics.107.086546 .
    • (2008) Genetics. , vol.179 , pp. 69-81
    • Casas-Mollano, J.A.1    Rohr, J.2    Kim, E.J.3    Balassa, E.4    Dijk, K.5    Cerutti, H.6
  • 54
    • 27944503390 scopus 로고    scopus 로고
    • REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii
    • Perez-Alegre M, Dubus A, Fernandez E. REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii. Mol Cell Biol. 2005;25:10628-38. doi: 10.1128/MCB.25.23.10628-10638.2005 .
    • (2005) Mol Cell Biol. , vol.25 , pp. 10628-10638
    • Perez-Alegre, M.1    Dubus, A.2    Fernandez, E.3
  • 55
    • 84922394706 scopus 로고    scopus 로고
    • sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software
    • Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC. sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res. 2015;42:e139. doi: 10.1093/nar/gku693 .
    • (2015) Nucleic Acids Res. , vol.42 , pp. e139
    • Kakrana, A.1    Hammond, R.2    Patel, P.3    Nakano, M.4    Meyers, B.C.5
  • 56
    • 84870515741 scopus 로고    scopus 로고
    • Dicer-like2 activity in Physcomitrella patens Dicer-like4 mutants causes severe developmental dysfunction and sterility
    • Arif MA, Fattash I, Ma Z, Cho SH, Beike AK, Reski R, et al. Dicer-like2 activity in Physcomitrella patens Dicer-like4 mutants causes severe developmental dysfunction and sterility. Mol Plant. 2012;5:1281-94. doi: 10.1093/mp/sss036 .
    • (2012) Mol Plant. , vol.5 , pp. 1281-1294
    • Arif, M.A.1    Fattash, I.2    Ma, Z.3    Cho, S.H.4    Beike, A.K.5    Reski, R.6
  • 57
    • 80052388966 scopus 로고    scopus 로고
    • RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function
    • Cerutti H, Ma X, Msanne J, Repas T. RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell. 2011;10:1164-72. doi: 10.1128/EC.05106-11 .
    • (2011) Eukaryot Cell. , vol.10 , pp. 1164-1172
    • Cerutti, H.1    Ma, X.2    Msanne, J.3    Repas, T.4
  • 58
    • 55249089227 scopus 로고    scopus 로고
    • Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice
    • Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK, et al. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics. 2008;9:451. doi: 10.1186/1471-2164-9-451 .
    • (2008) BMC Genomics , vol.9 , pp. 451
    • Kapoor, M.1    Arora, R.2    Lama, T.3    Nijhawan, A.4    Khurana, J.P.5    Tyagi, A.K.6
  • 59
    • 79958753423 scopus 로고    scopus 로고
    • Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize
    • Qian Y, Cheng Y, Cheng X, Jiang H, Zhu S, Cheng B. Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize. Plant Cell Rep. 2011;30:1347-63. doi: 10.1007/s00299-011-1046-6 .
    • (2011) Plant Cell Rep. , vol.30 , pp. 1347-1363
    • Qian, Y.1    Cheng, Y.2    Cheng, X.3    Jiang, H.4    Zhu, S.5    Cheng, B.6
  • 60
    • 84860552254 scopus 로고    scopus 로고
    • Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum
    • Bai M, Yang GS, Chen WT, Mao ZC, Kang HX, Chen GH, et al. Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum. Gene. 2012;501:52-62. doi: 10.1016/j.gene.2012.02.009 .
    • (2012) Gene. , vol.501 , pp. 52-62
    • Bai, M.1    Yang, G.S.2    Chen, W.T.3    Mao, Z.C.4    Kang, H.X.5    Chen, G.H.6
  • 61
    • 84930638367 scopus 로고    scopus 로고
    • The Comparative Sequencing of Plant Small RNAs website. [ http://smallRNA.udel.edu ].
  • 62
    • 84930668436 scopus 로고    scopus 로고
    • Gene Expression Omnibus
    • National Center for Biotechnology Information, Gene Expression Omnibus. [ http://www.ncbi.nlm.nih.gov/geo ].
  • 63
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25. doi: 10.1186/gb-2009-10-3-r25 .
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 64
    • 70350123865 scopus 로고    scopus 로고
    • Distinct extremely abundant siRNAs associated with cosuppression in petunia
    • De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, et al. Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA. 2009;15:1965-70. doi: 10.1261/rna.1706109 .
    • (2009) RNA. , vol.15 , pp. 1965-1970
    • Paoli, E.1    Dorantes-Acosta, A.2    Zhai, J.3    Accerbi, M.4    Jeong, D.H.5    Park, S.6
  • 65
    • 68149119262 scopus 로고    scopus 로고
    • Clusters and superclusters of phased small RNAs in the developing inflorescence of rice
    • Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V, et al. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 2009;19:1429-40. doi: 10.1101/gr.089854.108 .
    • (2009) Genome Res. , vol.19 , pp. 1429-1440
    • Johnson, C.1    Kasprzewska, A.2    Tennessen, K.3    Fernandes, J.4    Nan, G.L.5    Walbot, V.6
  • 66
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA, secondary structure server
    • Hofacker IL. Vienna RNA, secondary structure server. Nucleic Acids Res. 2003;31:3429-31. doi: 10.1093/nar/gkg599 .
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 67
    • 84930659744 scopus 로고    scopus 로고
    • miRBase. [ http://mirbase.org ].


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.