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Volumn 34, Issue 4, 2015, Pages 544-558

NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis

Author keywords

Alternative splicing; Elongation checkpoint; Transcription

Indexed keywords

ARABIDOPSIS THALIANA NTR1 PROTEIN; PROTEIN; PROTEIN DOG1; RNA POLYMERASE II; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; HISTIDINE-BINDING PROTEIN; PERIPLASMIC BINDING PROTEIN; RNA SPLICING;

EID: 84923083596     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.15252/embj.201489478     Document Type: Article
Times cited : (56)

References (70)
  • 3
    • 30044441988 scopus 로고    scopus 로고
    • The human SWI/SNF subunit Brm is a regulator of alternative splicing
    • Batsché E, Yaniv M, Muchardt C (2005) The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 13: 22-29
    • (2005) Nat Struct Mol Biol , vol.13 , pp. 22-29
    • Batsché, E.1    Yaniv, M.2    Muchardt, C.3
  • 4
    • 33750957114 scopus 로고    scopus 로고
    • Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis
    • Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci USA 103: 17042-17047
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17042-17047
    • Bentsink, L.1    Jowett, J.2    Hanhart, C.J.3    Koornneef, M.4
  • 9
    • 70449641057 scopus 로고    scopus 로고
    • Progression through the RNA Polymerase II CTD Cycle
    • Buratowski S (2009) Progression through the RNA Polymerase II CTD Cycle. Mol Cell 36: 541-546
    • (2009) Mol Cell , vol.36 , pp. 541-546
    • Buratowski, S.1
  • 10
    • 79958061525 scopus 로고    scopus 로고
    • The Prp19 complex is a novel transcription elongation factor required for TREX occupancy at transcribed genes
    • Chanarat S, Seizl M, Strässer K (2011) The Prp19 complex is a novel transcription elongation factor required for TREX occupancy at transcribed genes. Genes Dev 25: 1147-1158
    • (2011) Genes Dev , vol.25 , pp. 1147-1158
    • Chanarat, S.1    Seizl, M.2    Strässer, K.3
  • 11
    • 84896727449 scopus 로고    scopus 로고
    • A splicing-dependent transcriptional checkpoint associated with prespliceosome formation
    • Chathoth KT, Barrass JD, Webb S, Beggs JD (2014) A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. Mol Cell 53: 779-790
    • (2014) Mol Cell , vol.53 , pp. 779-790
    • Chathoth, K.T.1    Barrass, J.D.2    Webb, S.3    Beggs, J.D.4
  • 12
    • 79952440464 scopus 로고    scopus 로고
    • Structural basis of RNA polymerase II backtracking, arrest and reactivation
    • Cheung ACM, Cramer P (2011) Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 471: 249-253
    • (2011) Nature , vol.471 , pp. 249-253
    • Cheung, A.C.M.1    Cramer, P.2
  • 14
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • Crooks GE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190
    • (2004) Genome Res , vol.14 , pp. 1188-1190
    • Crooks, G.E.1
  • 15
    • 84876545043 scopus 로고    scopus 로고
    • Spliceosome database: A tool for tracking components of the spliceosome
    • Cvitkovic I, Jurica MS (2013) Spliceosome database: a tool for tracking components of the spliceosome. Nucleic Acids Res 41: D132-D141
    • (2013) Nucleic Acids Res , vol.41 , pp. D132-D141
    • Cvitkovic, I.1    Jurica, M.S.2
  • 18
    • 84864627155 scopus 로고    scopus 로고
    • Pax 3/7 BP Is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism
    • Diao Y, Guo X, Li Y, Sun K, Lu L, Jiang L, Fu X, Zhu H, Sun H, Wang H, Wu Z (2012) Pax 3/7 BP Is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Cell Stem Cell 11: 231-241
    • (2012) Cell Stem Cell , vol.11 , pp. 231-241
    • Diao, Y.1    Guo, X.2    Li, Y.3    Sun, K.4    Lu, L.5    Jiang, L.6    Fu, X.7    Zhu, H.8    Sun, H.9    Wang, H.10    Wu, Z.11
  • 21
    • 0026633013 scopus 로고
    • 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae
    • Exinger F, Lacroute F (1992) 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet 22: 9-11
    • (1992) Curr Genet , vol.22 , pp. 9-11
    • Exinger, F.1    Lacroute, F.2
  • 23
    • 0002386913 scopus 로고
    • 2 from contingency tables, and the calculation of P
    • 2 from contingency tables, and the calculation of P. J R Stat Soc 85: 87-94
    • (1922) J R Stat Soc , vol.85 , pp. 87-94
    • Fisher, R.A.1
  • 26
    • 0024520745 scopus 로고
    • Site-directed mutagenesis by overlap extension using the polymerase chain reaction
    • Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59
    • (1989) Gene , vol.77 , pp. 51-59
    • Ho, S.N.1    Hunt, H.D.2    Horton, R.M.3    Pullen, J.K.4    Pease, L.R.5
  • 27
    • 0041305816 scopus 로고    scopus 로고
    • Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae
    • Howe KJ, Kane CM, Ares M Jr (2003) Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9: 993-1006
    • (2003) RNA , vol.9 , pp. 993-1006
    • Howe, K.J.1    Kane, C.M.2    Ares, M.3
  • 29
    • 0026648570 scopus 로고
    • The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII
    • Izban MG, Luse DS (1992) The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII. Genes Dev 6: 1342-1356
    • (1992) Genes Dev , vol.6 , pp. 1342-1356
    • Izban, M.G.1    Luse, D.S.2
  • 30
    • 33947727751 scopus 로고    scopus 로고
    • Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans
    • Ji Q, Huang C-H, Peng J, Hashmi S, Ye T, Chen Y (2007) Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans. Exp Cell Res 313: 1460-1472
    • (2007) Exp Cell Res , vol.313 , pp. 1460-1472
    • Ji, Q.1    Huang, C.-H.2    Peng, J.3    Hashmi, S.4    Ye, T.5    Chen, Y.6
  • 33
    • 77749320166 scopus 로고    scopus 로고
    • Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
    • Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc 5: 457-472
    • (2010) Nat Protoc , vol.5 , pp. 457-472
    • Kaufmann, K.1    Muiño, J.M.2    Østerås, M.3    Farinelli, L.4    Krajewski, P.5    Angenent, G.C.6
  • 34
    • 0034307008 scopus 로고    scopus 로고
    • Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription
    • Komarnitsky P (2000) Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev 14: 2452-2460
    • (2000) Genes Dev , vol.14 , pp. 2452-2460
    • Komarnitsky, P.1
  • 35
    • 0027761185 scopus 로고
    • Disruption of base pairing between the 5′ splice site and the 5′ end of U1 snRNA is required for spliceosome assembly
    • Konforti BB, Koziolkiewicz MJ, Konarska MM (1993) Disruption of base pairing between the 5′ splice site and the 5′ end of U1 snRNA is required for spliceosome assembly. Cell 75: 863-873
    • (1993) Cell , vol.75 , pp. 863-873
    • Konforti, B.B.1    Koziolkiewicz, M.J.2    Konarska, M.M.3
  • 36
    • 77955488349 scopus 로고    scopus 로고
    • The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5′ splice site cleavage during premRNA splicing
    • Koodathingal P, Novak T, Piccirilli JA, Staley JP (2010) The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5′ splice site cleavage during premRNA splicing. Mol Cell 39: 385-395
    • (2010) Mol Cell , vol.39 , pp. 385-395
    • Koodathingal, P.1    Novak, T.2    Piccirilli, J.A.3    Staley, J.P.4
  • 37
    • 84896918727 scopus 로고    scopus 로고
    • Pre-mRNA splicing-modulatory pharmacophores: The total synthesis of herboxidiene, a pladienolide-herboxidiene hybrid analog and related derivatives
    • Lagisetti C, Yermolina MV, Sharma LK, Palacios G, Prigaro BJ, Webb TR (2014) Pre-mRNA splicing-modulatory pharmacophores: the total synthesis of herboxidiene, a pladienolide-herboxidiene hybrid analog and related derivatives. ACS Chem Biol 9: 643-648
    • (2014) ACS Chem Biol , vol.9 , pp. 643-648
    • Lagisetti, C.1    Yermolina, M.V.2    Sharma, L.K.3    Palacios, G.4    Prigaro, B.J.5    Webb, T.R.6
  • 38
    • 34250620427 scopus 로고    scopus 로고
    • The absence of histone H2B monoubiquitination in the Arabidopsis hub 1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy
    • Liu Y, Koornneef M, Soppe WJJ (2007) The absence of histone H2B monoubiquitination in the Arabidopsis hub 1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19: 433-444
    • (2007) Plant Cell , vol.19 , pp. 433-444
    • Liu, Y.1    Koornneef, M.2    Soppe, W.J.J.3
  • 39
    • 38349138023 scopus 로고    scopus 로고
    • An improved method for preparing Agrobacterium cells that simplifies the Arabidopsis transformation protocol
    • Logemann E, Birkenbihl RP, Ulker B, Somssich IE (2006 ) An improved method for preparing Agrobacterium cells that simplifies the Arabidopsis transformation protocol. Plant Methods 2: 16
    • (2006) Plant Methods , vol.2 , pp. 16
    • Logemann, E.1    Birkenbihl, R.P.2    Ulker, B.3    Somssich, I.E.4
  • 40
    • 84861890038 scopus 로고    scopus 로고
    • Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
    • Marquez Y, Brown JWS, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22: 1184-1195
    • (2012) Genome Res , vol.22 , pp. 1184-1195
    • Marquez, Y.1    Brown, J.W.S.2    Simpson, C.3    Barta, A.4    Kalyna, M.5
  • 41
    • 77953408963 scopus 로고    scopus 로고
    • Spliceosome discards intermediates via the DEAH box ATPase Prp43p
    • Mayas RM, Maita H, Semlow DR, Staley JP (2010) Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc Natl Acad Sci 107: 10020
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 10020
    • Mayas, R.M.1    Maita, H.2    Semlow, D.R.3    Staley, J.P.4
  • 42
    • 0026729490 scopus 로고
    • Herboxidiene, a new herbicidal substance from Streptomyces chromofuscus A7847. Taxonomy, fermentation, isolation, physico-chemical and biological properties
    • Miller-Wideman M, Makkar N, Tran M, Isaac B, Biest N, Stonard R (1992) Herboxidiene, a new herbicidal substance from Streptomyces chromofuscus A7847. Taxonomy, fermentation, isolation, physico-chemical and biological properties. J Antibiot (Tokyo) 45: 914-921
    • (1992) J Antibiot (Tokyo) , vol.45 , pp. 914-921
    • Miller-Wideman, M.1    Makkar, N.2    Tran, M.3    Isaac, B.4    Biest, N.5    Stonard, R.6
  • 43
    • 84890996756 scopus 로고    scopus 로고
    • The seed dormancy defect of Arabidopsis mutants lacking the transcript elongation factor TFIIS is caused by reduced expression of the DOG1 gene
    • Mortensen SA, Grasser KD (2014) The seed dormancy defect of Arabidopsis mutants lacking the transcript elongation factor TFIIS is caused by reduced expression of the DOG1 gene. FEBS Lett 588: 47-51
    • (2014) FEBS Lett , vol.588 , pp. 47-51
    • Mortensen, S.A.1    Grasser, K.D.2
  • 44
    • 33847661809 scopus 로고    scopus 로고
    • Protocol for the fast chromatin immunoprecipitation (ChIP) method
    • Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc 1: 179-185
    • (2006) Nat Protoc , vol.1 , pp. 179-185
    • Nelson, J.D.1    Denisenko, O.2    Bomsztyk, K.3
  • 46
    • 33847343883 scopus 로고    scopus 로고
    • Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: Regulation by hormones and stresses: Stress regulation of alternative splicing of SR genes
    • Palusa SG, Ali GS, Reddy ASN (2007 ) Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses: stress regulation of alternative splicing of SR genes. Plant J 49: 1091-1107
    • (2007) Plant J , vol.49 , pp. 1091-1107
    • Palusa, S.G.1    Ali, G.S.2    Reddy, A.S.N.3
  • 47
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 48
    • 33748766359 scopus 로고    scopus 로고
    • Inhibition of a spliceosome turnover pathway suppresses splicing defects
    • Pandit S, Lynn B, Rymond BC (2006) Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc Natl Acad Sci 103: 13700-13705
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 13700-13705
    • Pandit, S.1    Lynn, B.2    Rymond, B.C.3
  • 50
    • 0026697999 scopus 로고
    • Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II
    • Reines D (1992) Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J Biol Chem 267: 3795-3800
    • (1992) J Biol Chem , vol.267 , pp. 3795-3800
    • Reines, D.1
  • 51
    • 1342269199 scopus 로고    scopus 로고
    • Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil
    • Riles L, Shaw RJ, Johnston M, Reines D (2004) Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil. Yeast 21: 241-248
    • (2004) Yeast , vol.21 , pp. 241-248
    • Riles, L.1    Shaw, R.J.2    Johnston, M.3    Reines, D.4
  • 52
    • 84885128190 scopus 로고    scopus 로고
    • Analysis of long non-coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana
    • Rowley MJ, Böhmdorfer G, Wierzbicki AT (2013) Analysis of long non-coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana. Methods (San Diego Calif) 63: 160-169
    • (2013) Methods (San Diego Calif) , vol.63 , pp. 160-169
    • Rowley, M.J.1    Böhmdorfer, G.2    Wierzbicki, A.T.3
  • 53
    • 79952364016 scopus 로고    scopus 로고
    • Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons
    • Saint-André V, Batsché E, Rachez C, Muchardt C (2011) Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat Struct Mol Biol 18: 337-344
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 337-344
    • Saint-André, V.1    Batsché, E.2    Rachez, C.3    Muchardt, C.4
  • 55
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 56
    • 0017172263 scopus 로고
    • Purification of a factor from Ehrlich ascites tumor cells specifically stimulating RNA polymerase II
    • Sekimizu K, Kobayashi N, Mizuno D, Natori S (1976) Purification of a factor from Ehrlich ascites tumor cells specifically stimulating RNA polymerase II. Biochemistry (Mosc) 15: 5064-5070
    • (1976) Biochemistry (Mosc) , vol.15 , pp. 5064-5070
    • Sekimizu, K.1    Kobayashi, N.2    Mizuno, D.3    Natori, S.4
  • 57
    • 0026014804 scopus 로고
    • An efficient method for isolation of RNA from tissue cultured plant cells
    • Shirzadegan M, Christie P, Seemann JR (1991) An efficient method for isolation of RNA from tissue cultured plant cells. Nucleic Acids Res 19: 6055
    • (1991) Nucleic Acids Res , vol.19 , pp. 6055
    • Shirzadegan, M.1    Christie, P.2    Seemann, J.R.3
  • 59
    • 77950998789 scopus 로고    scopus 로고
    • Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability
    • Sigurdsson S, Dirac-Svejstrup AB, Svejstrup JQ (2010) Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability. Mol Cell 38: 202-210
    • (2010) Mol Cell , vol.38 , pp. 202-210
    • Sigurdsson, S.1    Dirac-Svejstrup, A.B.2    Svejstrup, J.Q.3
  • 61
    • 79952616415 scopus 로고    scopus 로고
    • Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes through altered transcript splicing
    • Swaraz AM, Park Y-D, Hur Y (2011) Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes through altered transcript splicing. Plant Sci. Int J Exp Plant Biol 180: 661-671
    • (2011) Plant Sci. Int J Exp Plant Biol , vol.180 , pp. 661-671
    • Swaraz, A.M.1    Park, Y.-D.2    Hur, Y.3
  • 62
    • 50849121749 scopus 로고    scopus 로고
    • TFIP11, CCNL1 and EWSR1 protein-protein interactions, and their nuclear localization
    • Tannukit S, Wen X, Wang H, Paine ML (2008) TFIP11, CCNL1 and EWSR1 protein-protein interactions, and their nuclear localization. Int J Mol Sci 9: 1504-1514
    • (2008) Int J Mol Sci , vol.9 , pp. 1504-1514
    • Tannukit, S.1    Wen, X.2    Wang, H.3    Paine, M.L.4
  • 63
    • 29144515824 scopus 로고    scopus 로고
    • Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2
    • Tsai R-T (2005) Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 19: 2991-3003
    • (2005) Genes Dev , vol.19 , pp. 2991-3003
    • Tsai, R.-T.1
  • 64
    • 54349105689 scopus 로고    scopus 로고
    • Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta
    • Waadt R, Schmidt LK, Lohse M, Hashimoto K, Bock R, Kudla J (2008) Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J Cell Mol Biol 56: 505-516
    • (2008) Plant J Cell Mol Biol , vol.56 , pp. 505-516
    • Waadt, R.1    Schmidt, L.K.2    Lohse, M.3    Hashimoto, K.4    Bock, R.5    Kudla, J.6
  • 65
    • 60349104299 scopus 로고    scopus 로고
    • The spliceosome: Design principles of a dynamic RNP machine
    • Wahl MC, Will CL, Lührmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701-718
    • (2009) Cell , vol.136 , pp. 701-718
    • Wahl, M.C.1    Will, C.L.2    Lührmann, R.3
  • 66
    • 18544374104 scopus 로고    scopus 로고
    • Structural organization and cellular localization of tuftelin-interacting protein 11 (TFIP11)
    • Wen X, Lei Y-P, Zhou YL, Okamoto CT, Snead ML, Paine ML (2005) Structural organization and cellular localization of tuftelin-interacting protein 11 (TFIP11). Cell Mol Life Sci 62: 1038-1046
    • (2005) Cell Mol Life Sci , vol.62 , pp. 1038-1046
    • Wen, X.1    Lei, Y.-P.2    Zhou, Y.L.3    Okamoto, C.T.4    Snead, M.L.5    Paine, M.L.6
  • 68
    • 84891150041 scopus 로고    scopus 로고
    • Identification of a novel component C2ORF3 in the lariat-intron complex: Lack of C2ORF 3 interferes with pre-mRNA splicing via intron turnover pathway
    • Yoshimoto R, Okawa K, Yoshida M, Ohno M, Kataoka N (2014) Identification of a novel component C2ORF3 in the lariat-intron complex: lack of C2ORF 3 interferes with pre-mRNA splicing via intron turnover pathway. Genes Cells 19: 78-87
    • (2014) Genes Cells , vol.19 , pp. 78-87
    • Yoshimoto, R.1    Okawa, K.2    Yoshida, M.3    Ohno, M.4    Kataoka, N.5


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