메뉴 건너뛰기




Volumn 32, Issue 7, 2015, Pages 1788-1799

Ancient origin and recent innovations of RNA polymerase IV and V

Author keywords

Escape from Adaptive Conflict; Gene duplication; RNA Polymerase IV; RNA Polymerase V; RNA Silencing; small RNA directed DNA methylation

Indexed keywords

ARGONAUTE PROTEIN; DICER; HOLOENZYME; NUCLEAR RNA POLYMERASE D; NUCLEAR RNA POLYMERASE E; RNA POLYMERASE; RNA POLYMERASE IV; RNA POLYMERASE V; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; DNA DIRECTED RNA POLYMERASE; PLANT PROTEIN; PROTEIN SUBUNIT;

EID: 84936866747     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv060     Document Type: Article
Times cited : (62)

References (69)
  • 1
    • 0037123639 scopus 로고    scopus 로고
    • RNA-dependent RNA polymerases, viruses, and RNA silencing
    • Ahlquist P. (2002). RNA-dependent RNA polymerases, viruses, and RNA silencing. Science 296: 1270-1273
    • (2002) Science , vol.296 , pp. 1270-1273
    • Ahlquist, P.1
  • 3
    • 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
  • 5
    • 84929650224 scopus 로고    scopus 로고
    • Evolution of the telomere-associated protein pot1a in arabidopsis thaliana is characterized by positive selection to reinforce protein-protein interaction
    • Beilstein MA, Renfrew KB, Song X, Shakirov EV, Zanis MJ, Shippen DE. (2015). Evolution of the telomere-associated protein POT1a in Arabidopsis thaliana is characterized by positive selection to reinforce protein-protein interaction. Mol Biol Evol. 32: 1329-1341
    • (2015) Mol Biol Evol , vol.32 , pp. 1329-1341
    • Beilstein, M.A.1    Renfrew, K.B.2    Song, X.3    Shakirov, E.V.4    Zanis, M.J.5    Shippen, D.E.6
  • 6
    • 67349099134 scopus 로고    scopus 로고
    • RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family
    • Bies-Etheve N, Pontier D, Lahmy S, Picart C, Vega D, Cooke R, Lagrange T. (2009). RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep. 10: 649-654
    • (2009) Embo Rep , vol.10 , pp. 649-654
    • Bies-Etheve, N.1    Pontier, D.2    Lahmy, S.3    Picart, C.4    Vega, D.5    Cooke, R.6    Lagrange, T.7
  • 7
    • 84896723632 scopus 로고    scopus 로고
    • A nuclear perspective on RNAi pathways in metazoans
    • Cecere G, Grishok A. (2014). A nuclear perspective on RNAi pathways in metazoans. Biochim Biophys Acta. 1839: 223-233
    • (2014) Biochim Biophys Acta , vol.1839 , pp. 223-233
    • Cecere, G.1    Grishok, A.2
  • 8
    • 58149163280 scopus 로고    scopus 로고
    • Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development
    • Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z, Frank W, Axtell MJ. (2008). Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet. 4: e1000314
    • (2008) Plos Genet , vol.4 , pp. e1000314
    • Cho, S.H.1    Addo-Quaye, C.2    Coruh, C.3    Arif, M.A.4    Ma, Z.5    Frank, W.6    Axtell, M.J.7
  • 9
    • 34547587566 scopus 로고    scopus 로고
    • Antiviral immunity directed by small RNAs
    • Ding SW, Voinnet O. (2007). Antiviral immunity directed by small RNAs. Cell 130: 413-426
    • (2007) Cell , vol.130 , pp. 413-426
    • Ding, S.W.1    Voinnet, O.2
  • 12
    • 3042666256 scopus 로고    scopus 로고
    • Muscle: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 14
    • 80053587336 scopus 로고    scopus 로고
    • AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana
    • Eun C, Lorkovic ZJ, Naumann U, Long Q, Havecker ER, Simon SA, Meyers BC, Matzke MA. (2011). AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One 6: e25730
    • (2011) Plos One , vol.6 , pp. e25730
    • Eun, C.1    Lorkovic, Z.J.2    Naumann, U.3    Long, Q.4    Havecker, E.R.5    Simon, S.A.6    Meyers, B.C.7    Matzke, M.A.8
  • 18
    • 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
    • Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. (2012). 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. 48: 811-818
    • (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
  • 20
    • 33745279055 scopus 로고    scopus 로고
    • Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning
    • Henderson IR, Johnson L, Zhang X, Lu C, Meyers BC, Green PJ, Jacobsen SE. (2006). Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet. 38: 721-725
    • (2006) Nat Genet , vol.38 , pp. 721-725
    • Henderson, I.R.1    Johnson, L.2    Zhang, X.3    Lu, C.4    Meyers, B.C.5    Green, P.J.6    Jacobsen, S.E.7
  • 21
    • 14844295120 scopus 로고    scopus 로고
    • RNA polymerase IV directs silencing of endogenous DNA
    • Herr AJ, Jensen M, Dalmay T, Baulcombe DC. (2005). RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120
    • (2005) Science , vol.308 , pp. 118-120
    • Herr, A.J.1    Jensen, M.2    Dalmay, T.3    Baulcombe, D.C.4
  • 22
    • 35148863240 scopus 로고    scopus 로고
    • Gene duplication and the adaptive evolution of a classic genetic switch
    • Hittinger CT, Carroll SB. (2007). Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677-681
    • (2007) Nature , vol.449 , pp. 677-681
    • Hittinger, C.T.1    Carroll, S.B.2
  • 25
    • 84901010244 scopus 로고    scopus 로고
    • Pol IV-dependent siRNA production is reduced in brassica rapa
    • Huang Y, Kendall T, Mosher R. (2013). Pol IV-dependent siRNA production is reduced in Brassica rapa. Biology 2: 1210-1223
    • (2013) Biology , vol.2 , pp. 1210-1223
    • Huang, Y.1    Kendall, T.2    Mosher, R.3
  • 26
    • 0028342845 scopus 로고
    • The evolution of functionally novel proteins after gene duplication
    • Hughes AL. (1994). The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 256: 119-124
    • (1994) Proc Biol Sci , vol.256 , pp. 119-124
    • Hughes, A.L.1
  • 27
    • 58749113430 scopus 로고    scopus 로고
    • A three-dimensional view of the molecular machinery of RNA interference
    • Jinek M, Doudna JA. (2009). A three-dimensional view of the molecular machinery of RNA interference. Nature 457: 405-412
    • (2009) Nature , vol.457 , pp. 405-412
    • Jinek, M.1    Doudna, J.A.2
  • 28
    • 77954426531 scopus 로고    scopus 로고
    • The evolution of a high copy gene array in arabidopsis
    • Kane J, Freeling M, Lyons E. (2010). The evolution of a high copy gene array in Arabidopsis. J Mol Evol. 70: 531-544
    • (2010) J Mol Evol , vol.70 , pp. 531-544
    • Kane, J.1    Freeling, M.2    Lyons, E.3
  • 29
    • 23744472834 scopus 로고    scopus 로고
    • A SNF2-like protein facilitates dynamic control of DNA methylation
    • Kanno T, Aufsatz W, Jaligot E, Mette MF, Matzke MA. (2005). A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep. 6: 649-655
    • (2005) Embo Rep , vol.6 , pp. 649-655
    • Kanno, T.1    Aufsatz, W.2    Jaligot, E.3    Mette, M.F.4    Matzke, M.A.5
  • 32
    • 58849120615 scopus 로고    scopus 로고
    • Polv(polivb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit
    • Lahmy S, Pontier D, Cavel E, Vega D, El-Shami M, Kanno T, Lagrange T. (2009). PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc Natl Acad Sci USA. 106: 941-946
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 941-946
    • Lahmy, S.1    Pontier, D.2    Cavel, E.3    Vega, D.4    El-Shami, M.5    Kanno, T.6    Lagrange, T.7
  • 35
    • 33845887976 scopus 로고    scopus 로고
    • Amultistep process gave rise to RNA polymerase IV of land plants
    • Luo J, Hall BD. (2007). Amultistep process gave rise to RNA polymerase IV of land plants. J Mol Evol. 64: 101-112
    • (2007) J Mol Evol , vol.64 , pp. 101-112
    • Luo, J.1    Hall, B.D.2
  • 36
    • 49649114289 scopus 로고    scopus 로고
    • Escape from adaptive conflict after duplication in an anthocyanin pathway gene
    • Marais Des DL, Rausher MD. (2008). Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765
    • (2008) Nature , vol.454 , pp. 762-765
    • Marais Des, D.L.1    Rausher, M.D.2
  • 37
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from highthroughput sequencing read
    • Martin M. (2011). Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet J. 17: 10-12
    • (2011) Embnet J. , vol.17 , pp. 10-12
    • Martin, M.1
  • 38
    • 84901041535 scopus 로고    scopus 로고
    • RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
    • Matzke MA, Mosher RA. (2014). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet. 15: 394-408
    • (2014) Nat Rev Genet , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 39
    • 84879414849 scopus 로고    scopus 로고
    • Argonaute proteins: Functional insights and emerging roles
    • Meister G. (2013). Argonaute proteins: functional insights and emerging roles. Nat Rev Genet. 14: 447-459
    • (2013) Nat Rev Genet , vol.14 , pp. 447-459
    • Meister, G.1
  • 40
    • 58749097426 scopus 로고    scopus 로고
    • Small RNAs in transcriptional gene silencing and genome defence
    • Moazed D. (2009). Small RNAs in transcriptional gene silencing and genome defence. Nature 457: 413-420
    • (2009) Nature , vol.457 , pp. 413-420
    • Moazed, D.1
  • 42
    • 77954735322 scopus 로고    scopus 로고
    • Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosper
    • Mosher RA. (2010). Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm. New Phytol. 186: 358-364
    • (2010) New Phytol , vol.186 , pp. 358-364
    • Mosher, R.A.1
  • 43
  • 44
    • 42549096814 scopus 로고    scopus 로고
    • PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
    • Mosher RA, Schwach F, Studholme D, Baulcombe DC. (2008). PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA. 105: 3145-3150
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 3145-3150
    • Mosher, R.A.1    Schwach, F.2    Studholme, D.3    Baulcombe, D.C.4
  • 45
    • 67650751542 scopus 로고    scopus 로고
    • Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
    • Neuwald AF. (2009). Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 25: 1869-1875
    • (2009) Bioinformatics , vol.25 , pp. 1869-1875
    • Neuwald, A.F.1
  • 48
    • 14844302397 scopus 로고    scopus 로고
    • Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation
    • Onodera Y, Haag JR, Ream TS, Nunes P, Pontes O, Pikaard CS. (2005). Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613-622
    • (2005) Cell , vol.120 , pp. 613-622
    • Onodera, Y.1    Haag, J.R.2    Ream, T.S.3    Nunes, P.4    Pontes, O.5    Pikaard, C.S.6
  • 49
    • 24344433177 scopus 로고    scopus 로고
    • Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in arabidopsis
    • Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T. (2005). Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19: 2030-2040
    • (2005) Genes Dev , vol.19 , pp. 2030-2040
    • Pontier, D.1    Yahubyan, G.2    Vega, D.3    Bulski, A.4    Saez-Vasquez, J.5    Hakimi, M.A.6    Lerbs-Mache, S.7    Colot, V.8    Lagrange, T.9
  • 50
    • 84908014725 scopus 로고    scopus 로고
    • Plant multisubunit RNA polymerases IV and V nucleic acid polymerases 30
    • Berlin) Heidelberg Springer
    • Ream TS, Haag JR, Pikaard CS. (2013). Plant multisubunit RNA polymerases IV and V Nucleic acid polymerases. Vol. 30. Nucleic acids and molecular biology. (Berlin) Heidelberg: Springer. p. 289-308
    • (2013) Nucleic Acids and Molecular Biology , pp. 289-308
    • Ream, T.S.1    Haag, J.R.2    Pikaard, C.S.3
  • 52
    • 84899513558 scopus 로고    scopus 로고
    • Deep conservation of human protein tandem repeats within the eukaryote
    • Schaper E, Gascuel O, Anisimova M. (2014). Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol. 31: 1132-1148
    • (2014) Mol Biol Evol , vol.31 , pp. 1132-1148
    • Schaper, E.1    Gascuel, O.2    Anisimova, M.3
  • 53
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder R, Edwards R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863-864
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 54
    • 73649130942 scopus 로고    scopus 로고
    • A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes
    • Sidorenko L, Dorweiler JE, Cigan AM, Arteaga-Vazquez M, Vyas M, Kermicle J, Jurcin D, Brzeski J, Cai Y, Chandler VL. (2009). A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes. PLoS Genet. 5: e1000725
    • (2009) Plos Genet , vol.5 , pp. e1000725
    • Sidorenko, L.1    Dorweiler, J.E.2    Cigan, A.M.3    Arteaga-Vazquez, M.4    Vyas, M.5    Kermicle, J.6    Jurcin, D.7    Brzeski, J.8    Cai, Y.9    Chandler, V.L.10
  • 55
    • 84866267075 scopus 로고    scopus 로고
    • Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness
    • Sikosek T, Chan HS, Bornberg-Bauer E. (2012). Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness. Proc Natl Acad Sci USA. 109: 14888-14893
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 14888-14893
    • Sikosek, T.1    Chan, H.S.2    Bornberg-Bauer, E.3
  • 56
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 57
    • 73649111706 scopus 로고    scopus 로고
    • Diversity of Pol IV function is defined by mutations at the maize rmr7 locus
    • Stonaker JL, Lim JP, Erhard KF, Hollick JB. (2009). Diversity of Pol IV function is defined by mutations at the maize rmr7 locus. PLoS Genet. 5: e1000706
    • (2009) Plos Genet , vol.5 , pp. e1000706
    • Stonaker, J.L.1    Lim, J.P.2    Erhard, K.F.3    Hollick, J.B.4
  • 58
    • 84861176807 scopus 로고    scopus 로고
    • Functional consequences of subunit diversity in RNA polymerases II and
    • Tan EH, Blevins T, Ream TS, Pikaard CS. (2012). Functional consequences of subunit diversity in RNA polymerases II and V. Cell Rep. 1: 208-214
    • (2012) Cell Rep , vol.1 , pp. 208-214
    • Tan, E.H.1    Blevins, T.2    Ream, T.S.3    Pikaard, C.S.4
  • 60
    • 79960725352 scopus 로고    scopus 로고
    • Evolutionary history of plant multisubunit RNA polymerases IV and V: Subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization
    • Tucker SL, Reece J, Ream TS, Pikaard CS. (2010). Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization. Cold Spring Harb Symp Quant Biol. 75: 285-297
    • (2010) Cold Spring Harb Symp Quant Biol , vol.75 , pp. 285-297
    • Tucker, S.L.1    Reece, J.2    Ream, T.S.3    Pikaard, C.S.4
  • 61
    • 46149088681 scopus 로고    scopus 로고
    • Plant argonautes
    • Vaucheret H. (2008). Plant ARGONAUTES. Trends Plant Sci. 13: 350-358
    • (2008) Trends Plant Sci , vol.13 , pp. 350-358
    • Vaucheret, H.1
  • 62
    • 84864950928 scopus 로고    scopus 로고
    • Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
    • Wan LC, Wang F, Guo X, Lu S, Qiu Z, Zhao Y, Zhang H, Lin J. (2012). Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing. BMC Plant Biol. 12: 146
    • (2012) BMC Plant Biol , vol.12 , pp. 146
    • Wan, L.C.1    Wang, F.2    Guo, X.3    Lu, S.4    Qiu, Z.5    Zhao, Y.6    Zhang, H.7    Lin, J.8
  • 63
    • 55449131096 scopus 로고    scopus 로고
    • Noncoding transcription by RNA polymerase pol IVb/pol V mediates transcriptional silencing of overlapping and adjacent genes
    • Wierzbicki AT, Haag JR, Pikaard CS. (2008). Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135: 635-648
    • (2008) Cell , vol.135 , pp. 635-648
    • Wierzbicki, A.T.1    Haag, J.R.2    Pikaard, C.S.3
  • 64
    • 67349112845 scopus 로고    scopus 로고
    • RNA polymerase v transcription guides argonaute4 to chromatin
    • Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. (2009). RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 41: 630-634
    • (2009) Nat Genet , vol.41 , pp. 630-634
    • Wierzbicki, A.T.1    Ream, T.S.2    Haag, J.R.3    Pikaard, C.S.4
  • 65
    • 84877766936 scopus 로고    scopus 로고
    • Molecular mechanisms of RNA interference
    • Wilson RC, Doudna JA. (2013). Molecular mechanisms of RNA interference. Annu Rev Biophys. 42: 217-239
    • (2013) Annu Rev Biophys , vol.42 , pp. 217-239
    • Wilson, R.C.1    Doudna, J.A.2
  • 67
    • 34547803197 scopus 로고    scopus 로고
    • Paml 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 68
    • 84871918724 scopus 로고    scopus 로고
    • Dynamic expression of small RNA populations in larch (larix leptolepis
    • Zhang J, Wu T, Li L, Han S, Li X, Zhang S, Qi L. (2013). Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta 237: 89-101
    • (2013) Planta , vol.237 , pp. 89-101
    • Zhang, J.1    Wu, T.2    Li, L.3    Han, S.4    Li, X.5    Zhang, S.6    Qi, L.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.