메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans

Author keywords

Argonaute protein; ChIP seq; Endo siRNA; Germline; Heterochromatin; Nuclear RNAi; PiRNA; Pre mRNA seq; Retrotransposon silencing; Transcriptional silencing

Indexed keywords

ARGONAUTE PROTEIN; HISTONE H3; HISTONE H3 LYSINE 9; HRDE 1 PROTEIN; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; WAGO 9 PROTEIN; CHROMATIN; HISTONE; LYSINE; RETROPOSON; RNA POLYMERASE II;

EID: 84926385395     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1157     Document Type: Article
Times cited : (39)

References (68)
  • 1
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391(6669):806-811.
    • (1998) Nature , vol.391 , Issue.6669 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 2
    • 0032443021 scopus 로고    scopus 로고
    • Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway
    • Kennerdell JR, Carthew RW: Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 1998, 95(7):1017-1026.
    • (1998) Cell , vol.95 , Issue.7 , pp. 1017-1026
    • Kennerdell, J.R.1    Carthew, R.W.2
  • 3
    • 0035905766 scopus 로고    scopus 로고
    • Role for a bidentate ribonuclease in the initiation step of RNA interference
    • Bernstein E, Caudy AA, Hammond SM, Hannon GJ: Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409(6818):363-366.
    • (2001) Nature , vol.409 , Issue.6818 , pp. 363-366
    • Bernstein, E.1    Caudy, A.A.2    Hammond, S.M.3    Hannon, G.J.4
  • 4
    • 0035839109 scopus 로고    scopus 로고
    • Argonaute2, a link between genetic and biochemical analyses of RNAi
    • Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ: Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 2001, 293(5532):1146-1150.
    • (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
  • 5
    • 0033572660 scopus 로고    scopus 로고
    • Targeted mRNA degradation by double-stranded RNA in vitro
    • Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA: Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 1999, 13(24):3191-3197.
    • (1999) Genes Dev , vol.13 , Issue.24 , pp. 3191-3197
    • Tuschl, T.1    Zamore, P.D.2    Lehmann, R.3    Bartel, D.P.4    Sharp, P.A.5
  • 6
    • 0034673638 scopus 로고    scopus 로고
    • An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells
    • Hammond SM, Bernstein E, Beach D, Hannon GJ: An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000, 404(6775):293-296.
    • (2000) Nature , vol.404 , Issue.6775 , pp. 293-296
    • Hammond, S.M.1    Bernstein, E.2    Beach, D.3    Hannon, G.J.4
  • 7
    • 0035863097 scopus 로고    scopus 로고
    • RNA interference is mediated by 21-and 22-nucleotide RNAs
    • Elbashir SM, Lendeckel W, Tuschl T: RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev 2001, 15(2):188-200.
    • (2001) Genes Dev , vol.15 , Issue.2 , pp. 188-200
    • Elbashir, S.M.1    Lendeckel, W.2    Tuschl, T.3
  • 8
    • 10944248935 scopus 로고    scopus 로고
    • Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs
    • Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D: Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 2004, 119(6):789-802.
    • (2004) Cell , vol.119 , Issue.6 , pp. 789-802
    • Motamedi, M.R.1    Verdel, A.2    Colmenares, S.U.3    Gerber, S.A.4    Gygi, S.P.5    Moazed, D.6
  • 9
    • 33846527241 scopus 로고    scopus 로고
    • Distinct populations of primary and secondary effectors during RNAi in C. elegans
    • Pak J, Fire A: Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 2007, 315(5809):241-244.
    • (2007) Science , vol.315 , Issue.5809 , pp. 241-244
    • Pak, J.1    Fire, A.2
  • 10
    • 33846524902 scopus 로고    scopus 로고
    • Secondary siRNAs result from unprimed RNA synthesis and form a distinct class
    • Sijen T, Steiner FA, Thijssen KL, Plasterk RH: Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 2007, 315(5809):244-247.
    • (2007) Science , vol.315 , Issue.5809 , pp. 244-247
    • Sijen, T.1    Steiner, F.A.2    Thijssen, K.L.3    Plasterk, R.H.4
  • 13
    • 78149476037 scopus 로고    scopus 로고
    • Small RNA-mediated quiescence of transposable elements in animals
    • Saito K, Siomi MC: Small RNA-mediated quiescence of transposable elements in animals. Dev Cell 2009, 19(5):687-697.
    • (2009) Dev Cell , vol.19 , Issue.5 , pp. 687-697
    • Saito, K.1    Siomi, M.C.2
  • 15
    • 79952818830 scopus 로고    scopus 로고
    • EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs
    • Maniar JM, Fire AZ: EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs. Curr Biol 2011, 21(6):449-459.
    • (2011) Curr Biol , vol.21 , Issue.6 , pp. 449-459
    • Maniar, J.M.1    Fire, A.Z.2
  • 17
    • 84890818459 scopus 로고    scopus 로고
    • The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression
    • Seth M, Shirayama M, Gu W, Ishidate T, Conte D Jr, Mello CC: The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression. Dev Cell 2013, 27(6):656-663.
    • (2013) Dev Cell , vol.27 , Issue.6 , pp. 656-663
    • Seth, M.1    Shirayama, M.2    Gu, W.3    Ishidate, T.4    Conte, D.5    Mello, C.C.6
  • 18
    • 84890836064 scopus 로고    scopus 로고
    • Protection of germline gene expression by the C. elegans Argonaute CSR-1
    • Wedeles CJ, Wu MZ, Claycomb JM: Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev Cell 2013, 27(6):664-671.
    • (2013) Dev Cell , vol.27 , Issue.6 , pp. 664-671
    • Wedeles, C.J.1    Wu, M.Z.2    Claycomb, J.M.3
  • 20
    • 0033832174 scopus 로고    scopus 로고
    • RNA-directed DNA methylation
    • Wassenegger M: RNA-directed DNA methylation. Plant Mol Biol 2000, 43(2-3):203-220.
    • (2000) Plant Mol Biol , vol.43 , Issue.2-3 , pp. 203-220
    • Wassenegger, M.1
  • 22
    • 58749097426 scopus 로고    scopus 로고
    • Small RNAs in transcriptional gene silencing and genome defence
    • Moazed D: Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457(7228):413-420.
    • (2009) Nature , vol.457 , Issue.7228 , pp. 413-420
    • Moazed, D.1
  • 23
    • 77952236323 scopus 로고    scopus 로고
    • RNAi-dependent formation of heterochromatin and its diverse functions
    • Grewal SI: RNAi-dependent formation of heterochromatin and its diverse functions. Curr Opin Genet Dev 2010, 20(2):134-141.
    • (2010) Curr Opin Genet Dev , vol.20 , Issue.2 , pp. 134-141
    • Grewal, S.I.1
  • 24
    • 84872533627 scopus 로고    scopus 로고
    • RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond
    • Castel SE, Martienssen RA: RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 2013, 14(2):100-112.
    • (2013) Nat Rev Genet , vol.14 , Issue.2 , pp. 100-112
    • Castel, S.E.1    Martienssen, R.A.2
  • 25
    • 33947273235 scopus 로고    scopus 로고
    • Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
    • Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ: Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007, 128(6):1089-1103.
    • (2007) Cell , vol.128 , Issue.6 , pp. 1089-1103
    • Brennecke, J.1    Aravin, A.A.2    Stark, A.3    Dus, M.4    Kellis, M.5    Sachidanandam, R.6    Hannon, G.J.7
  • 27
    • 84870060785 scopus 로고    scopus 로고
    • Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression
    • Sienski G, Donertas D, Brennecke J: Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 2012, 151(5):964-980.
    • (2012) Cell , vol.151 , Issue.5 , pp. 964-980
    • Sienski, G.1    Donertas, D.2    Brennecke, J.3
  • 29
    • 84874240831 scopus 로고    scopus 로고
    • Multiple roles for Piwi in silencing Drosophila transposons
    • Rozhkov NV, Hammell M, Hannon GJ: Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev 2013, 27(4):400-412.
    • (2013) Genes Dev , vol.27 , Issue.4 , pp. 400-412
    • Rozhkov, N.V.1    Hammell, M.2    Hannon, G.J.3
  • 30
    • 0032417618 scopus 로고    scopus 로고
    • RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans
    • Montgomery MK, Xu S, Fire A: RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci U S A 1998, 95(26):15502-15507.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.26 , pp. 15502-15507
    • Montgomery, M.K.1    Xu, S.2    Fire, A.3
  • 32
    • 0036499971 scopus 로고    scopus 로고
    • Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing
    • Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G: Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J 2002, 21(5):1121-1131.
    • (2002) EMBO J , vol.21 , Issue.5 , pp. 1121-1131
    • Schotta, G.1    Ebert, A.2    Krauss, V.3    Fischer, A.4    Hoffmann, J.5    Rea, S.6    Jenuwein, T.7    Dorn, R.8    Reuter, G.9
  • 34
    • 26444477370 scopus 로고    scopus 로고
    • Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila
    • Malone CD, Anderson AM, Motl JA, Rexer CH, Chalker DL: Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Mol Cell Biol 2005, 25(20):9151-9164.
    • (2005) Mol Cell Biol , vol.25 , Issue.20 , pp. 9151-9164
    • Malone, C.D.1    Anderson, A.M.2    Motl, J.A.3    Rexer, C.H.4    Chalker, D.L.5
  • 36
    • 77953961505 scopus 로고    scopus 로고
    • Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription
    • Guang S, Bochner AF, Burkhart KB, Burton N, Pavelec DM, Kennedy S: Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature 2010, 465(7301):1097-1101.
    • (2010) Nature , vol.465 , Issue.7301 , pp. 1097-1101
    • Guang, S.1    Bochner, A.F.2    Burkhart, K.B.3    Burton, N.4    Pavelec, D.M.5    Kennedy, S.6
  • 39
    • 84856239588 scopus 로고    scopus 로고
    • Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint
    • Gu SG, Pak J, Guang S, Maniar JM, Kennedy S, Fire A: Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. Nat Genet 2012, 44(2):157-164.
    • (2012) Nat Genet , vol.44 , Issue.2 , pp. 157-164
    • Gu, S.G.1    Pak, J.2    Guang, S.3    Maniar, J.M.4    Kennedy, S.5    Fire, A.6
  • 41
    • 84863631177 scopus 로고    scopus 로고
    • piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline
    • Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, Mello CC: piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 2012, 150(1):65-77.
    • (2012) Cell , vol.150 , Issue.1 , pp. 65-77
    • Shirayama, M.1    Seth, M.2    Lee, H.C.3    Gu, W.4    Ishidate, T.5    Conte, D.6    Mello, C.C.7
  • 43
    • 0017230019 scopus 로고
    • Development of the reproductive system of Caenorhabditis elegans
    • Hirsh D, Oppenheim D, Klass M: Development of the reproductive system of Caenorhabditis elegans. Dev Biol 1976, 49(1):200-219.
    • (1976) Dev Biol , vol.49 , Issue.1 , pp. 200-219
    • Hirsh, D.1    Oppenheim, D.2    Klass, M.3
  • 44
    • 74149094362 scopus 로고    scopus 로고
    • Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
    • Gu SG, Fire A: Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma 2010, 119(1):73-87.
    • (2010) Chromosoma , vol.119 , Issue.1 , pp. 73-87
    • Gu, S.G.1    Fire, A.2
  • 47
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman LS, Weissman JS: Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011, 469(7330):368-373.
    • (2011) Nature , vol.469 , Issue.7330 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 48
    • 0023138161 scopus 로고
    • Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes
    • Cai H, Luse DS: Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. J Biol Chem 1987, 262(1):298-304.
    • (1987) J Biol Chem , vol.262 , Issue.1 , pp. 298-304
    • Cai, H.1    Luse, D.S.2
  • 49
    • 0028090567 scopus 로고
    • Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing
    • Wuarin J, Schibler U: Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol Cell Biol 1994, 14(11):7219-7225.
    • (1994) Mol Cell Biol , vol.14 , Issue.11 , pp. 7219-7225
    • Wuarin, J.1    Schibler, U.2
  • 50
    • 0032741264 scopus 로고    scopus 로고
    • Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements
    • Bowen NJ, McDonald JF: Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res 1999, 9(10):924-935.
    • (1999) Genome Res , vol.9 , Issue.10 , pp. 924-935
    • Bowen, N.J.1    McDonald, J.F.2
  • 51
    • 0035208029 scopus 로고    scopus 로고
    • Evolutionary history of Cer elements and their impact on the C. elegans genome
    • Ganko EW, Fielman KT, McDonald JF: Evolutionary history of Cer elements and their impact on the C. elegans genome. Genome Res 2001, 11(12):2066-2074.
    • (2001) Genome Res , vol.11 , Issue.12 , pp. 2066-2074
    • Ganko, E.W.1    Fielman, K.T.2    McDonald, J.F.3
  • 52
    • 38449108664 scopus 로고    scopus 로고
    • Transposons in C.elegans
    • Bessereau JL: Transposons in C. elegans. WormBook 2006, 1-13.
    • (2006) WormBook , pp. 1-13
    • Bessereau, J.L.1
  • 54
    • 52949091512 scopus 로고    scopus 로고
    • Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7
    • Fischer SE, Butler MD, Pan Q, Ruvkun G: Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7. Nature 2008, 455(7212):491-496.
    • (2008) Nature , vol.455 , Issue.7212 , pp. 491-496
    • Fischer, S.E.1    Butler, M.D.2    Pan, Q.3    Ruvkun, G.4
  • 55
    • 33845436047 scopus 로고    scopus 로고
    • Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    • Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP: Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127(6):1193-1207.
    • (2006) Cell , vol.127 , Issue.6 , pp. 1193-1207
    • Ruby, J.G.1    Jan, C.2    Player, C.3    Axtell, M.J.4    Lee, W.5    Nusbaum, C.6    Ge, H.7    Bartel, D.P.8
  • 58
    • 84863624978 scopus 로고    scopus 로고
    • C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts
    • Lee HC, Gu W, Shirayama M, Youngman E, Conte D Jr, Mello CC: C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 2012, 150(1):78-87.
    • (2012) Cell , vol.150 , Issue.1 , pp. 78-87
    • Lee, H.C.1    Gu, W.2    Shirayama, M.3    Youngman, E.4    Conte, D.5    Mello, C.C.6
  • 60
    • 0032443562 scopus 로고    scopus 로고
    • A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal
    • Cox DN, Chao A, Baker J, Chang L, Qiao D, Lin H: A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 1998, 12(23):3715-3727.
    • (1998) Genes Dev , vol.12 , Issue.23 , pp. 3715-3727
    • Cox, D.N.1    Chao, A.2    Baker, J.3    Chang, L.4    Qiao, D.5    Lin, H.6
  • 62
    • 0028031830 scopus 로고
    • RNA-directed de novo methylation of genomic sequences in plants
    • Wassenegger M, Heimes S, Riedel L, Sanger HL: RNA-directed de novo methylation of genomic sequences in plants. Cell 1994, 76(3):567-576.
    • (1994) Cell , vol.76 , Issue.3 , pp. 567-576
    • Wassenegger, M.1    Heimes, S.2    Riedel, L.3    Sanger, H.L.4
  • 63
    • 0033832421 scopus 로고    scopus 로고
    • Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates
    • Matzke MA, Mette MF, Matzke AJ: Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Mol Biol 2000, 43(2-3):401-415.
    • (2000) Plant Mol Biol , vol.43 , Issue.2-3 , pp. 401-415
    • Matzke, M.A.1    Mette, M.F.2    Matzke, A.J.3
  • 67
    • 84861219911 scopus 로고    scopus 로고
    • C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon
    • Dennis S, Sheth U, Feldman JL, English KA, Priess JR: C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon. PLoS Pathog 2012, 8(3):e1002591.
    • (2012) PLoS Pathog , vol.8 , Issue.3
    • Dennis, S.1    Sheth, U.2    Feldman, J.L.3    English, K.A.4    Priess, J.R.5
  • 68
    • 0016063911 scopus 로고
    • The genetics of Caenorhabditis elegans
    • Brenner S: The genetics of Caenorhabditis elegans. Genetics 1974, 77(1):71-94.
    • (1974) Genetics , vol.77 , Issue.1 , pp. 71-94
    • Brenner, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.