메뉴 건너뛰기




Volumn 17, Issue 6, 2011, Pages 1012-1024

Plant siRNAs from introns mediate DNA methylation of host genes

Author keywords

DNA methylation; Intron; Mirtron; Plant; Sirtron; Small RNA

Indexed keywords

ARGONAUTE PROTEIN; DICER; MICRORNA 21; PLANT RNA; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; VEGETABLE PROTEIN;

EID: 79956227224     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2589011     Document Type: Article
Times cited : (34)

References (54)
  • 1
    • 34547668337 scopus 로고    scopus 로고
    • Common functions for diverse small RNAs of land plants
    • DOI 10.1105/tpc.107.051706
    • Axtell MJ, Snyder JA, Bartel DP. 2007. Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750-1769. (Pubitemid 47218838)
    • (2007) Plant Cell , vol.19 , Issue.6 , pp. 1750-1769
    • Axtell, M.J.1    Snyder, J.A.2    Bartel, D.P.3
  • 2
    • 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
  • 3
    • 13944260434 scopus 로고    scopus 로고
    • Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    • DOI 10.1261/rna.7240905
    • Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247. (Pubitemid 40270816)
    • (2005) RNA , vol.11 , Issue.3 , pp. 241-247
    • Baskerville, S.1    Bartel, D.P.2
  • 5
    • 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 JK. 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
  • 6
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • DOI 10.1093/bioinformatics/bth456
    • Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. 2004. GO:TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715. (Pubitemid 40136825)
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 8
    • 60149088848 scopus 로고    scopus 로고
    • Origins and Mechanisms of miRNAs and siRNAs
    • Carthew RW, Sontheimer EJ. 2009. Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 10
    • 77953903180 scopus 로고    scopus 로고
    • Small RNAs in angiosperms: Sequence characteristics, distribution and generation
    • Chen D, Meng Y, Ma X, Mao C, Bai Y, Cao J, Gu H, Wu P, Chen M. 2010. Small RNAs in angiosperms: sequence characteristics, distribution and generation. Bioinformatics 26: 1391-1394.
    • (2010) Bioinformatics , vol.26 , pp. 1391-1394
    • Chen, D.1    Meng, Y.2    Ma, X.3    Mao, C.4    Bai, Y.5    Cao, J.6    Gu, H.7    Wu, P.8    Chen, M.9
  • 11
    • 71949092231 scopus 로고    scopus 로고
    • A hairpin RNA construct residing in an intron efficiently triggered RNA-directed DNA methylation in tobacco
    • Dalakouras A, Moser M, Zwiebel M, Krczal G, Hell R, Wassenegger M. 2009. A hairpin RNA construct residing in an intron efficiently triggered RNA-directed DNA methylation in tobacco. Plant J 60: 840-851.
    • (2009) Plant J , vol.60 , pp. 840-851
    • Dalakouras, A.1    Moser, M.2    Zwiebel, M.3    Krczal, G.4    Hell, R.5    Wassenegger, M.6
  • 13
    • 23944483216 scopus 로고    scopus 로고
    • Partially redundant functions of arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-Acting siRNAs
    • DOI 10.1016/j.cub.2005.07.024, PII S0960982205007657
    • Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. 2005. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15: 1494-1500. (Pubitemid 41187489)
    • (2005) Current Biology , vol.15 , Issue.16 , pp. 1494-1500
    • Gasciolli, V.1    Mallory, A.C.2    Bartel, D.P.3    Vaucheret, H.4
  • 14
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: An expanding universe
    • Ghildiyal M, Zamore PD. 2009. Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108.
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 15
    • 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
  • 16
    • 77953808473 scopus 로고    scopus 로고
    • Next-generation genomics: An integrative approach
    • Hawkins RD, Hon GC, Ren B. 2010. Next-generation genomics: an integrative approach. Nat Rev Genet 11: 476-486.
    • (2010) Nat Rev Genet , vol.11 , pp. 476-486
    • Hawkins, R.D.1    Hon, G.C.2    Ren, B.3
  • 17
    • 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, Liang M, He H, Zhang H, Chen F, et al. 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
    • (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    Liang, M.7    He, H.8    Zhang, H.9    Chen, F.10
  • 18
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • DOI 10.1093/nar/gkg599
    • Hofacker IL. 2003. Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431. (Pubitemid 37442172)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 20
    • 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
    • doi: 10.1186/1471-2164-9-451
    • Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK, Kapoor S. 2008. 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 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    Kapoor, S.7
  • 24
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • doi: 10.1186/gb-2009-10-3-r25
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 25
    • 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 KH, Lee S, Baek SH, Kim VN. 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
  • 27
    • 36949014988 scopus 로고    scopus 로고
    • Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants
    • doi: 10.1371/journal.pcbi.0030238
    • Lindow M, Jacobsen A, Nygaard S, Mang Y, Krogh A. 2007. Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol 3: e238. doi: 10.1371/journal.pcbi.0030238.
    • (2007) PLoS Comput Biol , vol.3
    • Lindow, M.1    Jacobsen, A.2    Nygaard, S.3    Mang, Y.4    Krogh, A.5
  • 30
    • 0035984059 scopus 로고    scopus 로고
    • Endogenous and silencing-associated small RNAs in plants
    • DOI 10.1105/tpc.003210
    • Llave C, Kasschau KD, Rector MA, Carrington JC. 2002. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14: 1605-1619. (Pubitemid 34817147)
    • (2002) Plant Cell , vol.14 , Issue.7 , pp. 1605-1619
    • Llave, C.1    Kasschau, K.D.2    Rector, M.A.3    Carrington, J.C.4
  • 32
    • 41349114789 scopus 로고    scopus 로고
    • Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide
    • Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, et al. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127.
    • (2008) Cell , vol.133 , pp. 116-127
    • Mi, S.1    Cai, T.2    Hu, Y.3    Chen, Y.4    Hodges, E.5    Ni, F.6    Wu, L.7    Li, S.8    Zhou, H.9    Long, C.10
  • 33
    • 65349171662 scopus 로고    scopus 로고
    • An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites
    • Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T. 2009. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 28: 1078-1086.
    • (2009) EMBO J , vol.28 , pp. 1078-1086
    • Miura, A.1    Nakamura, M.2    Inagaki, S.3    Kobayashi, A.4    Saze, H.5    Kakutani, T.6
  • 34
    • 42449099982 scopus 로고    scopus 로고
    • Dual coding of siRNAs and miRNAs by plant transposable elements
    • DOI 10.1261/rna.916708
    • Piriyapongsa J, Jordan IK. 2008. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14: 814-821. (Pubitemid 351574902)
    • (2008) RNA , vol.14 , Issue.5 , pp. 814-821
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 35
    • 23044478505 scopus 로고    scopus 로고
    • Biochemical specialization within Arabidopsis RNA silencing pathways
    • DOI 10.1016/j.molcel.2005.06.014, PII S1097276505013936
    • Qi Y, Denli AM, Hannon GJ. 2005. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 19: 421-428. (Pubitemid 41074895)
    • (2005) Molecular Cell , vol.19 , Issue.3 , pp. 421-428
    • Qi, Y.1    Denli, A.M.2    Hannon, G.J.3
  • 36
    • 0026661135 scopus 로고
    • A spliced intron accumulates as a lariat in the nucleus of T cells
    • Qian L, Vu MN, Carter M, Wilkinson MF. 1992. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res 20: 5345-5350.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5345-5350
    • Qian, L.1    Vu, M.N.2    Carter, M.3    Wilkinson, M.F.4
  • 37
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • DOI 10.1101/gad.1476406
    • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20: 3407-3425. (Pubitemid 44969159)
    • (2006) Genes and Development , vol.20 , Issue.24 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 38
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 40
    • 44349094874 scopus 로고    scopus 로고
    • The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins
    • Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. 2008. The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant Cell Physiol 49: 493-500.
    • (2008) Plant Cell Physiol , vol.49 , pp. 493-500
    • Takeda, A.1    Iwasaki, S.2    Watanabe, T.3    Utsumi, M.4    Watanabe, Y.5
  • 41
    • 0037224921 scopus 로고    scopus 로고
    • A biochemical framework for RNA silencing in plants
    • DOI 10.1101/gad.1048103
    • Tang G, Reinhart BJ, Bartel DP, Zamore PD. 2003. A biochemical framework for RNA silencing in plants. Genes Dev 17: 49-63. (Pubitemid 36062508)
    • (2003) Genes and Development , vol.17 , Issue.1 , pp. 49-63
    • Tang, G.1    Reinhart, B.J.2    Bartel, D.P.3    Zamore, P.D.4
  • 42
    • 65349116002 scopus 로고    scopus 로고
    • Gene body DNA methylation in plants: A means to an end or an end to a means?
    • Teixeira FK, Colot V. 2009. Gene body DNA methylation in plants: a means to an end or an end to a means? EMBO J 28: 997-998.
    • (2009) EMBO J , vol.28 , pp. 997-998
    • Teixeira, F.K.1    Colot, V.2
  • 46
    • 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
  • 47
    • 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, He G, Sun H, Qi Y, Liu XS, Deng XW. 2009a. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21: 1053-1069.
    • (2009) Plant Cell , vol.21 , pp. 1053-1069
    • Wang, X.1    Elling, A.A.2    Li, X.3    Li, N.4    Peng, Z.5    He, G.6    Sun, H.7    Qi, Y.8    Liu, X.S.9    Deng, X.W.10
  • 48
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. 2009b. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 49
    • 73249125240 scopus 로고    scopus 로고
    • Rice MicroRNA effector complexes and targets
    • Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. 2009. Rice MicroRNA effector complexes and targets. Plant Cell 21: 3421-3435.
    • (2009) Plant Cell , vol.21 , pp. 3421-3435
    • Wu, L.1    Zhang, Q.2    Zhou, H.3    Ni, F.4    Wu, X.5    Qi, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.