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Volumn 11, Issue 7, 2014, Pages 793-797

Emerging roles of RNA processing factors in regulating long non-coding RNAs

Author keywords

Long non coding RNA; Pol IV; Pol V; RNA retention; RNA directed DNA methylation; Rrp6; Splicing; Transcriptional silencing

Indexed keywords

DNA BINDING PROTEIN; DNA METHYLTRANSFERASE; DOUBLE STRANDED RNA; LONG UNTRANSLATED RNA; RNA DIRECTED RNA POLYMERASE; RNA POLYMERASE; RNA PRECURSOR; SMALL INTERFERING RNA; SPACER DNA; ARABIDOPSIS PROTEIN; CHROMATIN; PLANT RNA;

EID: 84907543143     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.29731     Document Type: Note
Times cited : (22)

References (40)
  • 1
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • PMID:20142834
    • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010; 11:204-20; PMID:20142834; http://dx.doi.org/10.1038/nrg2719
    • (2010) Nat Rev Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 2
    • 79955120337 scopus 로고    scopus 로고
    • RNA-directed DNA methylation
    • PMID:21420348
    • Zhang H, Zhu JK. RNA-directed DNA methylation. Curr Opin Plant Biol 2011; 14:142-7; PMID:21420348; http://dx.doi.org/10.1016/j.pbi.2011.02.003
    • (2011) Curr Opin Plant Biol , vol.14 , pp. 142-147
    • Zhang, H.1    Zhu, J.K.2
  • 3
    • 84881520399 scopus 로고    scopus 로고
    • A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation
    • PMID:23567894
    • Pikaard CS, Haag JR, Pontes OM, Blevins T, Cocklin R. A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation. Cold Spring Harb Symp Quant Biol 2012; 77:205-12; PMID:23567894; http://dx.doi.org/10.1101/sqb.2013.77.014803
    • (2012) Cold Spring Harb Symp Quant Biol , vol.77 , pp. 205-212
    • Pikaard, C.S.1    Haag, J.R.2    Pontes, O.M.3    Blevins, T.4    Cocklin, R.5
  • 4
    • 84901041535 scopus 로고    scopus 로고
    • RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
    • PMID:24805120
    • Matzke MA, Mosher RA. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 2014; 15:394-408; http://dx.doi.org/10.1038/nrg3683; PMID:24805120
    • (2014) Nat Rev Genet , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 7
    • 34249330696 scopus 로고    scopus 로고
    • Epigenetic inheritance in plants
    • PMID:17522675
    • Henderson IR, Jacobsen SE. Epigenetic inheritance in plants. Nature 2007; 447:418-24; PMID:17522675; http://dx.doi.org/10.1038/nature05917
    • (2007) Nature , vol.447 , pp. 418-424
    • Henderson, I.R.1    Jacobsen, S.E.2
  • 8
    • 34248340993 scopus 로고    scopus 로고
    • Role of RNA polymerase IV in plant small RNA metabolism
    • PMID:17360559
    • Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A 2007; 104:4536-41; PMID:17360559; http://dx.doi.org/10.1073/pnas.0611456104
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 4536-4541
    • Zhang, X.1    Henderson, I.R.2    Lu, C.3    Green, P.J.4    Jacobsen, S.E.5
  • 9
    • 42549096814 scopus 로고    scopus 로고
    • PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
    • PMID:18287047
    • Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A 2008; 105:3145-50; PMID:18287047; http://dx.doi.org/10.1073/pnas.0709632105
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 3145-3150
    • Mosher, R.A.1    Schwach, F.2    Studholme, D.3    Baulcombe, D.C.4
  • 10
    • 34347382532 scopus 로고    scopus 로고
    • An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis
    • PMID:17526749
    • Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 2007; 19:1507-21; PMID:17526749; http://dx.doi.org/10.1105/tpc.107.051540
    • (2007) Plant Cell , vol.19 , pp. 1507-1521
    • Smith, L.M.1    Pontes, O.2    Searle, I.3    Yelina, N.4    Yousafzai, F.K.5    Herr, A.J.6    Pikaard, C.S.7    Baulcombe, D.C.8
  • 11
    • 79960960568 scopus 로고    scopus 로고
    • SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV
    • PMID:21811420
    • Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet 2011; 7:e1002195; PMID:21811420; http://dx.doi.org/10.1371/journal.pgen.1002195
    • (2011) PLoS Genet , vol.7 , pp. e1002195
    • Law, J.A.1    Vashisht, A.A.2    Wohlschlegel, J.A.3    Jacobsen, S.E.4
  • 13
    • 84877866795 scopus 로고    scopus 로고
    • DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV
    • PMID:23637343
    • Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, et al. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A 2013; 110:8290-5; PMID:23637343; http://dx.doi.org/10.1073/pnas.1300585110
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 8290-8295
    • Zhang, H.1    Ma, Z.Y.2    Zeng, L.3    Tanaka, K.4    Zhang, C.J.5    Ma, J.6    Bai, G.7    Wang, P.8    Zhang, S.W.9    Liu, Z.W.10
  • 16
    • 55449131096 scopus 로고    scopus 로고
    • Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes
    • PMID:19013275
    • Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008; 135:635-48; PMID:19013275; http://dx.doi.org/10.1016/j.cell.2008.09.035
    • (2008) Cell , vol.135 , pp. 635-648
    • Wierzbicki, A.T.1    Haag, J.R.2    Pikaard, C.S.3
  • 17
    • 67349112845 scopus 로고    scopus 로고
    • RNA polymerase V transcription guides ARGONAUTE4 to chromatin
    • PMID:19377477
    • Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 2009; 41:630-4; PMID:19377477; http://dx.doi.org/10.1038/ng.365
    • (2009) Nat Genet , vol.41 , pp. 630-634
    • Wierzbicki, A.T.1    Ream, T.S.2    Haag, J.R.3    Pikaard, C.S.4
  • 18
    • 84869489307 scopus 로고    scopus 로고
    • The role of long non-coding RNA in transcriptional gene silencing
    • PMID:22960034
    • Wierzbicki AT. The role of long non-coding RNA in transcriptional gene silencing. Curr Opin Plant Biol 2012; 15:517-22; PMID:22960034; http://dx.doi.org/10.1016/j.pbi.2012.08.008
    • (2012) Curr Opin Plant Biol , vol.15 , pp. 517-522
    • Wierzbicki, A.T.1
  • 19
    • 77953129746 scopus 로고    scopus 로고
    • A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis
    • PMID:20409711
    • Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis. Curr Biol 2010; 20:951-6; PMID:20409711; http://dx.doi.org/10.1016/j.cub.2010.03.062
    • (2010) Curr Biol , vol.20 , pp. 951-956
    • Law, J.A.1    Ausin, I.2    Johnson, L.M.3    Vashisht, A.A.4    Zhu, J.K.5    Wohlschlegel, J.A.6    Jacobsen, S.E.7
  • 20
    • 84893801023 scopus 로고    scopus 로고
    • The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci
    • PMID:24465213
    • Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L, Chen S, Huang HW, Cai T, He XJ. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet 2014; 10:e1003948; PMID:24465213; http://dx.doi.org/10.1371/journal.pgen.1003948
    • (2014) PLoS Genet , vol.10 , pp. e1003948
    • Liu, Z.W.1    Shao, C.R.2    Zhang, C.J.3    Zhou, J.X.4    Zhang, S.W.5    Li, L.6    Chen, S.7    Huang, H.W.8    Cai, T.9    He, X.J.10
  • 22
    • 8644233945 scopus 로고    scopus 로고
    • The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides
    • PMID:15604652
    • Aufsatz W, Mette MF, Matzke AJ, Matzke M. The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 2004; 54:793-804; PMID:15604652; http://dx.doi.org/10.1007/s11103-004-0179-1
    • (2004) Plant Mol Biol , vol.54 , pp. 793-804
    • Aufsatz, W.1    Mette, M.F.2    Matzke, A.J.3    Matzke, M.4
  • 23
    • 84899910150 scopus 로고    scopus 로고
    • An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis
    • PMID:24726328
    • Zhang H, Tang K, Qian W, Duan CG, Wang B, Zhang H, Wang P, Zhu X, Lang Z, Yang Y, et al. An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol Cell 2014; 54:418-30; PMID:24726328; http://dx.doi.org/10.1016/j.molcel.2014.03.019
    • (2014) Mol Cell , vol.54 , pp. 418-430
    • Zhang, H.1    Tang, K.2    Qian, W.3    Duan, C.G.4    Wang, B.5    Zhang, H.6    Wang, P.7    Zhu, X.8    Lang, Z.9    Yang, Y.10
  • 24
    • 51549111789 scopus 로고    scopus 로고
    • Quality control of mRNP in the nucleus
    • PMID:18563427
    • Schmid M, Jensen TH. Quality control of mRNP in the nucleus. Chromosoma 2008; 117:419-29; PMID:18563427; http://dx.doi.org/10.1007/s00412-008-0166-4
    • (2008) Chromosoma , vol.117 , pp. 419-429
    • Schmid, M.1    Jensen, T.H.2
  • 25
    • 79960681216 scopus 로고    scopus 로고
    • Rrp6, rrp47 and cofactors of the nuclear exosome
    • PMID:21713680
    • Butler JS, Mitchell P. Rrp6, rrp47 and cofactors of the nuclear exosome. Adv Exp Med Biol 2011; 702:91-104; PMID:21713680; http://dx.doi.org/10.1007/978-1-4419-7841-7-8
    • (2011) Adv Exp Med Biol , vol.702 , pp. 91-104
    • Butler, J.S.1    Mitchell, P.2
  • 26
    • 37349038984 scopus 로고    scopus 로고
    • Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
    • PMID:18160042
    • Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, et al. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 2007; 131:1340-53; PMID:18160042; http://dx.doi.org/10.1016/j.cell.2007.10.056
    • (2007) Cell , vol.131 , pp. 1340-1353
    • Chekanova, J.A.1    Gregory, B.D.2    Reverdatto, S.V.3    Chen, H.4    Kumar, R.5    Hooker, T.6    Yazaki, J.7    Li, P.8    Skiba, N.9    Peng, Q.10
  • 27
    • 60549114880 scopus 로고    scopus 로고
    • Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    • PMID:19169244
    • Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009; 457:1038-42; PMID:19169244; http://dx.doi.org/10.1038/nature07747
    • (2009) Nature , vol.457 , pp. 1038-1042
    • Neil, H.1    Malabat, C.2    D'Aubenton-Carafa, Y.3    Xu, Z.4    Steinmetz, L.M.5    Jacquier, A.6
  • 30
    • 40149112047 scopus 로고    scopus 로고
    • Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana
    • PMID:18266474
    • Li CF, Henderson IR, Song L, Fedoroff N, Lagrange T, Jacobsen SE. Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet 2008; 4:e27; PMID:18266474; http://dx.doi.org/10.1371/journal.pgen.0040027
    • (2008) PLoS Genet , vol.4 , pp. e27
    • Li, C.F.1    Henderson, I.R.2    Song, L.3    Fedoroff, N.4    Lagrange, T.5    Jacobsen, S.E.6
  • 31
  • 32
    • 84870942752 scopus 로고    scopus 로고
    • In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing
    • PMID:23142082
    • Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell 2012; 48:811-8; PMID:23142082; http://dx.doi.org/10.1016/j.molcel.2012.09.027
    • (2012) Mol Cell , vol.48 , pp. 811-818
    • Haag, J.R.1    Ream, T.S.2    Marasco, M.3    Nicora, C.D.4    Norbeck, A.D.5    Pasa-Tolic, L.6    Pikaard, C.S.7
  • 33
    • 64049086954 scopus 로고    scopus 로고
    • SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies
    • PMID:19332064
    • Kumakura N, Takeda A, Fujioka Y, Motose H, Takano R, Watanabe Y. SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies. FEBS Lett 2009; 583:1261-6; PMID:19332064; http://dx.doi.org/10.1016/j.febslet.2009.03.055
    • (2009) FEBS Lett , vol.583 , pp. 1261-1266
    • Kumakura, N.1    Takeda, A.2    Fujioka, Y.3    Motose, H.4    Takano, R.5    Watanabe, Y.6
  • 34
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: An expanding universe
    • PMID:19148191
    • Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet 2009; 10:94-108; PMID:19148191; http://dx.doi.org/10.1038/nrg2504
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 35
    • 84884697862 scopus 로고    scopus 로고
    • A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis
    • PMID:24068953
    • Huang CF, Miki D, Tang K, Zhou HR, Zheng Z, Chen W, Ma ZY, Yang L, Zhang H, Liu R, et al. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet 2013; 9:e1003779; PMID:24068953; http://dx.doi.org/10.1371/journal.pgen.1003779
    • (2013) PLoS Genet , vol.9 , pp. e1003779
    • Huang, C.F.1    Miki, D.2    Tang, K.3    Zhou, H.R.4    Zheng, Z.5    Chen, W.6    Ma, Z.Y.7    Yang, L.8    Zhang, H.9    Liu, R.10
  • 36
    • 84885901219 scopus 로고    scopus 로고
    • The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs
    • PMID:23877244
    • Dou K, Huang CF, Ma ZY, Zhang CJ, Zhou JX, Huang HW, Cai T, Tang K, Zhu JK, He XJ. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Nucleic Acids Res 2013; 41:8489-502; PMID:23877244; http://dx.doi.org/10.1093/nar/gkt639
    • (2013) Nucleic Acids Res , vol.41 , pp. 8489-8502
    • Dou, K.1    Huang, C.F.2    Ma, Z.Y.3    Zhang, C.J.4    Zhou, J.X.5    Huang, H.W.6    Cai, T.7    Tang, K.8    Zhu, J.K.9    He, X.J.10
  • 37
    • 33745690105 scopus 로고    scopus 로고
    • The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center
    • PMID:16839878
    • Pontes O, Li CF, Costa Nunes P, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006; 126:79-92; PMID:16839878; http://dx.doi.org/10.1016/j.cell.2006.05.031
    • (2006) Cell , vol.126 , pp. 79-92
    • Pontes, O.1    Li, C.F.2    Costa Nunes, P.3    Haag, J.4    Ream, T.5    Vitins, A.6    Jacobsen, S.E.7    Pikaard, C.S.8
  • 38
    • 84876419021 scopus 로고    scopus 로고
    • The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis
    • PMID:23524848
    • Zhang CJ, Zhou JX, Liu J, Ma ZY, Zhang SW, Dou K, Huang HW, Cai T, Liu R, Zhu JK, et al. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. EMBO J 2013; 32:1128-40; PMID:23524848; http://dx.doi.org/10.1038/emboj.2013.49
    • (2013) EMBO J , vol.32 , pp. 1128-1140
    • Zhang, C.J.1    Zhou, J.X.2    Liu, J.3    Ma, Z.Y.4    Zhang, S.W.5    Dou, K.6    Huang, H.W.7    Cai, T.8    Liu, R.9    Zhu, J.K.10
  • 39
    • 84863038938 scopus 로고    scopus 로고
    • The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis
    • PMID:22274613
    • Ausin I, Greenberg MV, Li CF, Jacobsen SE. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis. Epigenetics 2012; 7:29-33; PMID:22274613; http://dx.doi.org/10.4161/epi.7.1.18782
    • (2012) Epigenetics , vol.7 , pp. 29-33
    • Ausin, I.1    Greenberg, M.V.2    Li, C.F.3    Jacobsen, S.E.4
  • 40
    • 80053567859 scopus 로고    scopus 로고
    • Intron splicing suppresses RNA silencing in Arabidopsis
    • PMID:21689169
    • Christie M, Croft LJ, Carroll BJ. Intron splicing suppresses RNA silencing in Arabidopsis. Plant J 2011; 68:159-67; PMID:21689169; http://dx.doi.org/10.1111/j.1365-313X.2011.04676.x
    • (2011) Plant J , vol.68 , pp. 159-167
    • Christie, M.1    Croft, L.J.2    Carroll, B.J.3


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