메뉴 건너뛰기




Volumn 9, Issue 4, 2014, Pages

Extending the sRNAome of apple by next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; SMALL INTERFERING RNA; SMALL UNTRANSLATED RNA; PLANT RNA;

EID: 84899667863     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095782     Document Type: Article
Times cited : (17)

References (78)
  • 1
    • 38549093645 scopus 로고    scopus 로고
    • GDR (Genome Database for Rosaceae): Integrated web-database for Rosaceae genomics and genetics data
    • DOI 10.1093/nar/gkm803
    • Jung S, Staton M, Lee T, Blenda A, Svancara R, et al. (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-1040. (Pubitemid 351149864)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Jung, S.1    Staton, M.2    Lee, T.3    Blenda, A.4    Svancara, R.5    Abbott, A.6    Main, D.7
  • 2
    • 77957560949 scopus 로고    scopus 로고
    • The genome of the domesticated apple (Malus x domestica Borkh.)
    • Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, et al. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42: 833-839.
    • (2010) Nat Genet , vol.42 , pp. 833-839
    • Velasco, R.1    Zharkikh, A.2    Affourtit, J.3    Dhingra, A.4    Cestaro, A.5
  • 3
    • 78651293534 scopus 로고    scopus 로고
    • miRBase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 4
    • 84858746853 scopus 로고    scopus 로고
    • The transcriptomes of columnar and standard type apple trees (Malus x domestica) - A comparative study
    • Krost C, Petersen R, Schmidt ER (2012) The transcriptomes of columnar and standard type apple trees (Malus x domestica) - a comparative study. Gene 498: 223-230.
    • (2012) Gene , vol.498 , pp. 223-230
    • Krost, C.1    Petersen, R.2    Schmidt, E.R.3
  • 5
    • 84862232060 scopus 로고    scopus 로고
    • Apple miRNAs and tasiRNAs with novel regulatory networks
    • Xia R, Zhu H, An Y, Beers EP, Liu Z (2012) Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol 13: R47.
    • (2012) Genome Biol , vol.13
    • Xia, R.1    Zhu, H.2    An, Y.3    Beers, E.P.4    Liu, Z.5
  • 6
    • 84872616417 scopus 로고    scopus 로고
    • Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies
    • Krost C, Petersen R, Lokan S, Brauksiepe B, Braun P, et al. (2013) Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies. Plant Mol Biol 81: 211-220.
    • (2013) Plant Mol Biol , vol.81 , pp. 211-220
    • Krost, C.1    Petersen, R.2    Lokan, S.3    Brauksiepe, B.4    Braun, P.5
  • 7
    • 0034596989 scopus 로고    scopus 로고
    • Transcriptional silencing and promoter methylation triggered by double-stranded RNA
    • Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19: 5194-5201.
    • (2000) EMBO J , vol.19 , pp. 5194-5201
    • Mette, M.F.1    Aufsatz, W.2    Van Der Winden, J.3    Matzke, M.A.4    Matzke, A.J.5
  • 8
    • 0033615491 scopus 로고    scopus 로고
    • A species of small antisense RNA in posttranscriptional gene silencing in plants
    • Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950-952.
    • (1999) Science , vol.286 , pp. 950-952
    • Hamilton, A.J.1    Baulcombe, D.C.2
  • 9
    • 0035839109 scopus 로고    scopus 로고
    • Argonaute2, a link between genetic and biochemical analyses of RNAi
    • DOI 10.1126/science.1064023
    • Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146-1150. (Pubitemid 32758097)
    • (2001) Science , vol.293 , Issue.5532 , pp. 1146-1150
    • Hammond, S.M.1    Boettcher, S.2    Caudy, A.A.3    Kobayashi, R.4    Hannon, G.J.5
  • 10
    • 0034673638 scopus 로고    scopus 로고
    • An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells
    • DOI 10.1038/35005107
    • Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293-296. (Pubitemid 30163547)
    • (2000) Nature , vol.404 , Issue.6775 , pp. 293-296
    • Hammond, S.M.1    Bernstein, E.2    Beach, D.3    Hannon, G.J.4
  • 11
    • 0942279635 scopus 로고    scopus 로고
    • RNAi-mediated targeting of heterochromatin by the RITS complex
    • Verdel A (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676.
    • (2004) Science , vol.303 , pp. 672-676
    • Verdel, A.1
  • 12
    • 77951974552 scopus 로고    scopus 로고
    • DNA methylation mediated by a microRNA pathway
    • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, et al. (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38: 465-475.
    • (2010) Mol Cell , vol.38 , pp. 465-475
    • Wu, L.1    Zhou, H.2    Zhang, Q.3    Zhang, J.4    Ni, F.5
  • 14
    • 8144225486 scopus 로고    scopus 로고
    • MicroRNA genes are transcribed by RNA polymerase II
    • DOI 10.1038/sj.emboj.7600385
    • Lee Y, Kim M, Han J, Yeom K-H, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060. (Pubitemid 39472426)
    • (2004) EMBO Journal , vol.23 , Issue.20 , pp. 4051-4060
    • Lee, Y.1    Kim, M.2    Han, J.3    Yeom, K.-H.4    Lee, S.5    Baek, S.H.6    Kim, V.N.7
  • 15
    • 29144528351 scopus 로고    scopus 로고
    • Expression of Arabidopsis miRNA genes
    • Xie Z (2005) Expression of Arabidopsis miRNA genes. PLANT Physiol 138: 2145-2154.
    • (2005) PLANT Physiol , vol.138 , pp. 2145-2154
    • Xie, Z.1
  • 16
    • 0036645146 scopus 로고    scopus 로고
    • MicroRNAs in plants
    • Reinhart BJ (2002) MicroRNAs in plants. Genes Dev 16: 1616-1626.
    • (2002) Genes Dev , vol.16 , pp. 1616-1626
    • Reinhart, B.J.1
  • 18
    • 84877677064 scopus 로고    scopus 로고
    • Classification and comparison of small RNAs from plants
    • Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64: 137-159.
    • (2013) Annu Rev Plant Biol , vol.64 , pp. 137-159
    • Axtell, M.J.1
  • 19
    • 29244490062 scopus 로고    scopus 로고
    • Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    • DOI 10.1016/j.cell.2005.11.035, PII S0092867405013309
    • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291. (Pubitemid 41821785)
    • (2005) Cell , vol.123 , Issue.7 , pp. 1279-1291
    • Borsani, O.1    Zhu, J.2    Verslues, P.E.3    Sunkar, R.4    Zhu, J.-K.5
  • 20
    • 82955207556 scopus 로고    scopus 로고
    • MicroRNAs as master regulators of the plant NB-LRR defence gene family via the production of phased, trans-acting siRNAs
    • Zhai J, Jeong D-H, De Paoli E, Park S, Rosen BD, et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defence gene family via the production of phased, trans-acting siRNAs. Genes Dev 25: 2540-2553.
    • (2011) Genes Dev , vol.25 , pp. 2540-2553
    • Zhai, J.1    Jeong, D.-H.2    De Paoli, E.3    Park, S.4    Rosen, B.D.5
  • 22
    • 0037009520 scopus 로고    scopus 로고
    • Two classes of short interfering RNA in RNA silencing
    • DOI 10.1093/emboj/cdf464
    • Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21: 4671-4679. (Pubitemid 34984354)
    • (2002) EMBO Journal , vol.21 , Issue.17 , pp. 4671-4679
    • Hamilton, A.1    Voinnet, O.2    Chappell, L.3    Baulcombe, D.4
  • 25
    • 84872413149 scopus 로고    scopus 로고
    • Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches
    • Li Y-F, Zheng Y, Jagadeeswaran G, Sunkar R (2013) Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. Plant Sci 203-204: 17-24.
    • (2013) Plant Sci , vol.203-204 , pp. 17-24
    • Li, Y.-F.1    Zheng, Y.2    Jagadeeswaran, G.3    Sunkar, R.4
  • 26
    • 84873905119 scopus 로고    scopus 로고
    • Profiling and identification of small rDNA-derived RNAs and their potential biological functions
    • Wei H, Zhou B, Zhang F, Tu Y, Hu Y, et al. (2013) Profiling and identification of small rDNA-derived RNAs and their potential biological functions. PLoS ONE 8: e56842.
    • (2013) PLoS ONE , vol.8
    • Wei, H.1    Zhou, B.2    Zhang, F.3    Tu, Y.4    Hu, Y.5
  • 27
    • 56049119367 scopus 로고    scopus 로고
    • Stress-induced tRNA-derived RNAs: A novel class of small RNAs in the primitive eukaryote Giardia lamblia
    • Li Y, Luo J, Zhou H, Liao J-Y, Ma L-M, et al. (2008) Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia. Nucleic Acids Res 36: 6048-6055.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6048-6055
    • Li, Y.1    Luo, J.2    Zhou, H.3    Liao, J.-Y.4    Ma, L.-M.5
  • 28
    • 71049136041 scopus 로고    scopus 로고
    • Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing
    • Hsieh L-C, Lin S-I, Shih AC-C, Chen J-W, Lin W-Y, et al. (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. PLANT Physiol 151: 2120-2132.
    • (2009) PLANT Physiol , vol.151 , pp. 2120-2132
    • Hsieh, L.-C.1    Lin, S.-I.2    Shih, A.C.-C.3    Chen, J.-W.4    Lin, W.-Y.5
  • 29
    • 59449092339 scopus 로고    scopus 로고
    • Structure and function of homodomain-leucine zipper (HD-Zip) proteins
    • Elhiti M, Stasolla C (2009) Structure and function of homodomain-leucine zipper (HD-Zip) proteins. Plant Signal Behav 4: 86.
    • (2009) Plant Signal Behav , vol.4 , pp. 86
    • Elhiti, M.1    Stasolla, C.2
  • 30
    • 50649110065 scopus 로고    scopus 로고
    • A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    • Zhu Q-H, 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 Res 18: 1456-1465.
    • (2008) Genome Res , vol.18 , pp. 1456-1465
    • Zhu, Q.-H.1    Spriggs, A.2    Matthew, L.3    Fan, L.4    Kennedy, G.5
  • 31
    • 84874331148 scopus 로고    scopus 로고
    • Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing
    • Zhang R, Marshall D, Bryan GJ, Hornyik C (2013) Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS ONE 8: e57233.
    • (2013) PLoS ONE , vol.8
    • Zhang, R.1    Marshall, D.2    Bryan, G.J.3    Hornyik, C.4
  • 32
    • 36849089069 scopus 로고    scopus 로고
    • A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation
    • DOI 10.1111/j.1365-313X.2007.03309.x
    • Zubko E, Meyer P (2007) A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation. Plant J 52: 1131-1139. (Pubitemid 350231159)
    • (2007) Plant Journal , vol.52 , Issue.6 , pp. 1131-1139
    • Zubko, E.1    Meyer, P.2
  • 33
    • 77952415941 scopus 로고    scopus 로고
    • Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis
    • Ron M, Alandete Saez M, Eshed Williams L, Fletcher JC, McCormick S (2010) Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev 24: 1010-1021.
    • (2010) Genes Dev , vol.24 , pp. 1010-1021
    • Ron, M.1    Alandete Saez, M.2    Eshed Williams, L.3    Fletcher, J.C.4    McCormick, S.5
  • 35
    • 84879780279 scopus 로고    scopus 로고
    • Identification of ta-siRNAs and cis-nat-siRNAs in cassava and their roles in response to cassava bacterial blight
    • Quintero A, Pérez-Quintero AL, López C (2013) Identification of ta-siRNAs and cis-nat-siRNAs in cassava and their roles in response to cassava bacterial blight. Genomics Proteomics Bioinformatics 11: 172-181.
    • (2013) Genomics Proteomics Bioinformatics , vol.11 , pp. 172-181
    • Quintero, A.1    Pérez-Quintero, A.L.2    López, C.3
  • 36
    • 72049103210 scopus 로고    scopus 로고
    • Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis
    • Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, et al. (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 61: 165-177.
    • (2010) J Exp Bot , vol.61 , pp. 165-177
    • Moldovan, D.1    Spriggs, A.2    Yang, J.3    Pogson, B.J.4    Dennis, E.S.5
  • 37
    • 33845395154 scopus 로고    scopus 로고
    • Prediction of trans-antisense transcripts in Arabidopsis thaliana
    • Wang H, Chua N-H, Wang X-J (2006) Prediction of trans-antisense transcripts in Arabidopsis thaliana . Genome Biol 7: R92.
    • (2006) Genome Biol , vol.7
    • Wang, H.1    Chua, N.-H.2    Wang, X.-J.3
  • 38
    • 61449191758 scopus 로고    scopus 로고
    • Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
    • Zhou X, Sunkar R, Jin H, Zhu J-K, Zhang W (2009) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa . Genome Res 19: 70-78.
    • (2009) Genome Res , vol.19 , pp. 70-78
    • Zhou, X.1    Sunkar, R.2    Jin, H.3    Zhu, J.-K.4    Zhang, W.5
  • 39
    • 84876685658 scopus 로고    scopus 로고
    • Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)
    • Zheng H, Qiyan J, Zhiyong N, Hui Z (2013) Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max). BMC Genomics 14: 280.
    • (2013) BMC Genomics , vol.14 , pp. 280
    • Zheng, H.1    Qiyan, J.2    Zhiyong, N.3    Hui, Z.4
  • 40
    • 84871390926 scopus 로고    scopus 로고
    • Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
    • Lu T, Zhu C, Lu G, Guo Y, Zhou Y, et al. (2012) Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice. BMC Genomics 13: 721.
    • (2012) BMC Genomics , vol.13 , pp. 721
    • Lu, T.1    Zhu, C.2    Lu, G.3    Guo, Y.4    Zhou, Y.5
  • 42
    • 84875754164 scopus 로고    scopus 로고
    • Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis
    • Zhan S, Lukens L (2013) Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis. PLANT Physiol 161: 2171-2180.
    • (2013) PLANT Physiol , vol.161 , pp. 2171-2180
    • Zhan, S.1    Lukens, L.2
  • 43
    • 24644448635 scopus 로고    scopus 로고
    • Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
    • Wang X-J, Gaasterland T, Chua N-H (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol 6: R30.
    • (2005) Genome Biol , vol.6
    • Wang, X.-J.1    Gaasterland, T.2    Chua, N.-H.3
  • 44
    • 84862209063 scopus 로고    scopus 로고
    • PlantNATsDB: A comprehensive database of plant natural antisense transcripts
    • Chen D, Yuan C, Zhang J, Zhang Z, Bai L, et al. (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res 40: D1187-D1193.
    • (2012) Nucleic Acids Res , vol.40
    • Chen, D.1    Yuan, C.2    Zhang, J.3    Zhang, Z.4    Bai, L.5
  • 45
    • 17444430392 scopus 로고    scopus 로고
    • microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    • DOI 10.1016/j.cell.2005.04.004
    • Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221. (Pubitemid 40546389)
    • (2005) Cell , vol.121 , Issue.2 , pp. 207-221
    • Allen, E.1    Xie, Z.2    Gustafson, A.M.3    Carrington, J.C.4
  • 46
    • 69949093486 scopus 로고    scopus 로고
    • Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families
    • Jagadeeswaran G, Zheng Y, Li Y-F, Shukla LI, Matts J, et al. (2009) Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 184: 85-98.
    • (2009) New Phytol , vol.184 , pp. 85-98
    • Jagadeeswaran, G.1    Zheng, Y.2    Li, Y.-F.3    Shukla, L.I.4    Matts, J.5
  • 47
    • 84873033996 scopus 로고    scopus 로고
    • miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens
    • Cho SH, Coruh C, Axtell MJ (2012) miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens . Plant Cell 24: 4837-4849.
    • (2012) Plant Cell , vol.24 , pp. 4837-4849
    • Cho, S.H.1    Coruh, C.2    Axtell, M.J.3
  • 48
    • 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 G-L, et al. (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 19: 1429-1440.
    • (2009) Genome Res , vol.19 , pp. 1429-1440
    • Johnson, C.1    Kasprzewska, A.2    Tennessen, K.3    Fernandes, J.4    Nan, G.-L.5
  • 49
    • 77955186909 scopus 로고    scopus 로고
    • TAS1 trans-acting siRNA targets are differentially regulated at low temperature, and TAS1 trans-acting siRNA mediates temperature-controlled At1g51679 expression
    • Kume K, Tsutsumi K, Saitoh Y (2010) TAS1 trans-acting siRNA targets are differentially regulated at low temperature, and TAS1 trans-acting siRNA mediates temperature-controlled At1g51679 expression. Biosci Biotechnol Biochem 74: 1435-1440.
    • (2010) Biosci Biotechnol Biochem , vol.74 , pp. 1435-1440
    • Kume, K.1    Tsutsumi, K.2    Saitoh, Y.3
  • 50
    • 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
    • DOI 10.1105/tpc.107.050062
    • Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, et al. (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell Online 19: 926-942. (Pubitemid 46953238)
    • (2007) Plant Cell , vol.19 , Issue.3 , 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    Kasschau, K.D.7    Carrington, J.C.8
  • 51
    • 84870453549 scopus 로고    scopus 로고
    • Identification of trans-acting siRNAs and their regulatory cascades in grapevine
    • Zhang C, Li G, Wang J, Fang J (2012) Identification of trans-acting siRNAs and their regulatory cascades in grapevine. Bioinformatics 28: 2561-2568.
    • (2012) Bioinformatics , vol.28 , pp. 2561-2568
    • Zhang, C.1    Li, G.2    Wang, J.3    Fang, J.4
  • 52
    • 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, et al. (2013) MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. Plant Cell 25: 1555-1572.
    • (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
  • 55
    • 84878460609 scopus 로고    scopus 로고
    • A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species
    • Kallman T, Chen J, Gyllenstrand N, Lagercrantz U (2013) A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. PLANT Physiol 162: 741-754.
    • (2013) PLANT Physiol , vol.162 , pp. 741-754
    • Kallman, T.1    Chen, J.2    Gyllenstrand, N.3    Lagercrantz, U.4
  • 57
    • 84865097020 scopus 로고    scopus 로고
    • Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs
    • Zhu H, Xia R, Zhao B, An Y, Dardick CD, et al. (2012) Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol 12: 149.
    • (2012) BMC Plant Biol , vol.12 , pp. 149
    • Zhu, H.1    Xia, R.2    Zhao, B.3    An, Y.4    Dardick, C.D.5
  • 58
    • 84887025720 scopus 로고    scopus 로고
    • Trans-acting small interfering RNA4: Key to nutraceutical synthesis in grape development?
    • Rock CD (2013) Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends Plant Sci 18: 601-610.
    • (2013) Trends Plant Sci , vol.18 , pp. 601-610
    • Rock, C.D.1
  • 59
    • 24944491201 scopus 로고    scopus 로고
    • A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis
    • Yoshikawa M (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19: 2164-2175.
    • (2005) Genes Dev , vol.19 , pp. 2164-2175
    • Yoshikawa, M.1
  • 60
    • 33750440526 scopus 로고    scopus 로고
    • A Two-Hit Trigger for siRNA Biogenesis in Plants
    • DOI 10.1016/j.cell.2006.09.032, PII S009286740601292X
    • Axtell MJ, Jan C, Rajagopalan R, Bartel DP (2006) A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577. (Pubitemid 44647429)
    • (2006) Cell , vol.127 , Issue.3 , pp. 565-577
    • Axtell, M.J.1    Jan, C.2    Rajagopalan, R.3    Bartel, D.P.4
  • 61
    • 84864455779 scopus 로고    scopus 로고
    • Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis
    • Rajeswaran R, Aregger M, Zvereva AS, Borah BK, Gubaeva EG, et al. (2012) Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res 40: 6241-6254.
    • (2012) Nucleic Acids Res , vol.40 , pp. 6241-6254
    • Rajeswaran, R.1    Aregger, M.2    Zvereva, A.S.3    Borah, B.K.4    Gubaeva, E.G.5
  • 62
    • 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 D-H, et al. (2009) Distinct extremely abundant siRNAs associated with cosuppression in Petunia. RNA 15: 1965-1970.
    • (2009) RNA , vol.15 , pp. 1965-1970
    • De Paoli, E.1    Dorantes-Acosta, A.2    Zhai, J.3    Accerbi, M.4    Jeong, D.-H.5
  • 64
    • 84867651695 scopus 로고    scopus 로고
    • Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection
    • Romanel E, Silva TF, Corrêa RL, Farinelli L, Hawkins JS, et al. (2012) Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. Plant Mol Biol 80: 443-460.
    • (2012) Plant Mol Biol , vol.80 , pp. 443-460
    • Romanel, E.1    Silva, T.F.2    Corrêa, R.L.3    Farinelli, L.4    Hawkins, J.S.5
  • 65
    • 0034743135 scopus 로고    scopus 로고
    • Characterisation of pericentromeric and sticky intercalary heterochromatin in Ornithogalum longibracteatum (Hyacinthaceae)
    • Pedrosa A, Jantsch MF, Moscone EA, Ambros PF, Schweizer D (2001) Characterisation of pericentrometric and sticky intercalary heterochromatin in Ornithogalum longibracteatum (Hyacinthaceae). Chromosoma 110: 203-213. (Pubitemid 32700414)
    • (2001) Chromosoma , vol.110 , Issue.3 , pp. 203-213
    • Pedrosa, A.1    Jantsch, M.F.2    Moscone, E.A.3    Ambros, P.F.4    Schweizer, D.5
  • 66
    • 59349118366 scopus 로고    scopus 로고
    • Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
    • Slotkin RK, Vaughn M, Borges F, Tanurdžić M, Becker JD, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
    • (2009) Cell , vol.136 , pp. 461-472
    • Slotkin, R.K.1    Vaughn, M.2    Borges, F.3    Tanurdžić, M.4    Becker, J.D.5
  • 67
    • 66149176899 scopus 로고    scopus 로고
    • Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize
    • Wang X, Elling AA, Li X, Li N, Peng Z, et al. (2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell Online 21: 1053-1069.
    • (2009) Plant Cell Online , vol.21 , pp. 1053-1069
    • Wang, X.1    Elling, A.A.2    Li, X.3    Li, N.4    Peng, Z.5
  • 68
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12.
    • (2011) EMBnet.Journal , vol.17 , pp. 10-12
    • Martin, M.1
  • 70
    • 79959953839 scopus 로고    scopus 로고
    • miRanalyzer: An update on the detection and analysis of microRNAs in high-throughput sequencing experiments
    • Hackenberg M, Rodríguez-Ezpeleta N, Aransay AM (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 39: W132-138.
    • (2011) Nucleic Acids Res , vol.39
    • Hackenberg, M.1    Rodríguez-Ezpeleta, N.2    Aransay, A.M.3
  • 71
    • 84878022987 scopus 로고    scopus 로고
    • ShortStack: Comprehensive annotation and quantification of small RNA genes
    • Axtell MJ (2013) ShortStack: Comprehensive annotation and quantification of small RNA genes. RNA 19: 740-751.
    • (2013) RNA , vol.19 , pp. 740-751
    • Axtell, M.J.1
  • 73
    • 79959967431 scopus 로고    scopus 로고
    • psRNATarget: A plant small RNA target analysis server
    • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155-W159.
    • (2011) Nucleic Acids Res , vol.39
    • Dai, X.1    Zhao, P.X.2
  • 74
    • 58049220318 scopus 로고    scopus 로고
    • CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets
    • Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25: 130-131.
    • (2009) Bioinformatics , vol.25 , pp. 130-131
    • Addo-Quaye, C.1    Miller, W.2    Axtell, M.J.3
  • 75
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybridization
    • Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol Clifton NJ 453: 3-31.
    • (2008) Methods Mol Biol Clifton NJ , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 78
    • 42349111552 scopus 로고    scopus 로고
    • A universal classification of eukaryotic transposable elements implemented in Repbase
    • DOI 10.1038/nrg2165-c1, PII NRG2165C1
    • Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9: 411-412. (Pubitemid 351556058)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.5 , pp. 411-412
    • Kapitonov, V.V.1    Jurka, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.