메뉴 건너뛰기




Volumn 205-206, Issue , 2013, Pages 55-62

Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants

Author keywords

DsRNase; MiRNA; PARS; PIP seq; Post transcriptional regulation; RNA genomics; RNA secondary structure; RNA silencing; RNA binding proteins; SiRNA; Small RNAs; SsRNase

Indexed keywords

MESSENGER RNA; PLANT RNA; RNA BINDING PROTEIN; TRANSCRIPTOME;

EID: 84874431413     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2013.01.009     Document Type: Review
Times cited : (38)

References (99)
  • 1
    • 1642458353 scopus 로고    scopus 로고
    • RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon
    • Buratti E., et al. RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Mol. Cell. Biol. 2004, 24:1387-1400.
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 1387-1400
    • Buratti, E.1
  • 3
    • 60149112933 scopus 로고    scopus 로고
    • The dynamic landscapes of RNA architecture
    • Cruz J.A., Westhof E. The dynamic landscapes of RNA architecture. Cell 2009, 136:604-609.
    • (2009) Cell , vol.136 , pp. 604-609
    • Cruz, J.A.1    Westhof, E.2
  • 4
    • 60149103676 scopus 로고    scopus 로고
    • The centrality of RNA
    • Sharp P.A. The centrality of RNA. Cell 2009, 136:577-580.
    • (2009) Cell , vol.136 , pp. 577-580
    • Sharp, P.A.1
  • 5
    • 80055088036 scopus 로고    scopus 로고
    • The ribosome: a molecular machine powered by RNA
    • Trappl K., Polacek N. The ribosome: a molecular machine powered by RNA. Met. Ions Life Sci. 2011, 9:253-275.
    • (2011) Met. Ions Life Sci. , vol.9 , pp. 253-275
    • Trappl, K.1    Polacek, N.2
  • 6
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff L.A., et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:9362-9367.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1
  • 7
    • 79958269950 scopus 로고    scopus 로고
    • RNA-protein interactions in human health and disease
    • Khalil A.M., Rinn J.L. RNA-protein interactions in human health and disease. Semin. Cell Dev. Biol. 2011, 22:359-365.
    • (2011) Semin. Cell Dev. Biol. , vol.22 , pp. 359-365
    • Khalil, A.M.1    Rinn, J.L.2
  • 8
    • 84860765680 scopus 로고    scopus 로고
    • Systematic discovery of structural elements governing stability of mammalian messenger RNAs
    • Goodarzi H., et al. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 2012, 485:264-268.
    • (2012) Nature , vol.485 , pp. 264-268
    • Goodarzi, H.1
  • 9
    • 84861121932 scopus 로고    scopus 로고
    • Global analysis of RNA secondary structure in two metazoans
    • Li F., et al. Global analysis of RNA secondary structure in two metazoans. Cell Rep. 2012, 1:69-82.
    • (2012) Cell Rep. , vol.1 , pp. 69-82
    • Li, F.1
  • 10
    • 84871887837 scopus 로고    scopus 로고
    • Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome
    • Li F., et al. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 2012, 24:4346-4359.
    • (2012) Plant Cell , vol.24 , pp. 4346-4359
    • Li, F.1
  • 11
    • 0035912793 scopus 로고    scopus 로고
    • Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome
    • Keene J.D. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:7018-7024.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 7018-7024
    • Keene, J.D.1
  • 13
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: coordination of post-transcriptional events
    • Keene J.D. RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 2007, 8:533-543.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 14
    • 44449166478 scopus 로고    scopus 로고
    • RNA-binding proteins and post-transcriptional gene regulation
    • Glisovic T., Bachorik J.L., Yong J., Dreyfuss G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett. 2008, 582:1977-1986.
    • (2008) FEBS Lett. , vol.582 , pp. 1977-1986
    • Glisovic, T.1    Bachorik, J.L.2    Yong, J.3    Dreyfuss, G.4
  • 15
    • 0018879004 scopus 로고
    • Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits
    • Kozak M. Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits. Cell 1980, 19:79-90.
    • (1980) Cell , vol.19 , pp. 79-90
    • Kozak, M.1
  • 16
    • 0005218668 scopus 로고
    • Influences of mRNA secondary structure on initiation by eukaryotic ribosomes
    • Kozak M. Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc. Natl. Acad. Sci. U.S.A. 1986, 83:2850-2854.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 2850-2854
    • Kozak, M.1
  • 17
    • 4644242349 scopus 로고    scopus 로고
    • RNA silencing in plants
    • Baulcombe D. RNA silencing in plants. Nature 2004, 431:356-363.
    • (2004) Nature , vol.431 , pp. 356-363
    • Baulcombe, D.1
  • 18
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    • Jones-Rhoades M.W., Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 2004, 14:787-799.
    • (2004) Mol. Cell , vol.14 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 19
    • 84862591360 scopus 로고    scopus 로고
    • Molecular recognition and function of riboswitches
    • Serganov A., Patel D.J. Molecular recognition and function of riboswitches. Curr. Opin. Struct. Biol. 2012, 22:279-286.
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 279-286
    • Serganov, A.1    Patel, D.J.2
  • 20
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • Breaker R.R. Prospects for riboswitch discovery and analysis. Mol. Cell 2011, 43:867-879.
    • (2011) Mol. Cell , vol.43 , pp. 867-879
    • Breaker, R.R.1
  • 21
    • 18744396047 scopus 로고    scopus 로고
    • Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria
    • Mironov A.S., et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 2002, 111:747-756.
    • (2002) Cell , vol.111 , pp. 747-756
    • Mironov, A.S.1
  • 22
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419:952-956.
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 23
    • 36248989143 scopus 로고    scopus 로고
    • Riboswitch-dependent gene regulation and its evolution in the plant kingdom
    • Bocobza S., et al. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev. 2007, 21:2874-2879.
    • (2007) Genes Dev. , vol.21 , pp. 2874-2879
    • Bocobza, S.1
  • 24
    • 37849045636 scopus 로고    scopus 로고
    • Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs
    • Wachter A., et al. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell 2007, 19:3437-3450.
    • (2007) Plant Cell , vol.19 , pp. 3437-3450
    • Wachter, A.1
  • 25
    • 34548712632 scopus 로고    scopus 로고
    • Searching genomes for ribozymes and riboswitches
    • Hammann C., Westhof E. Searching genomes for ribozymes and riboswitches. Genome Biol. 2007, 8:210.
    • (2007) Genome Biol. , vol.8 , pp. 210
    • Hammann, C.1    Westhof, E.2
  • 26
    • 0030266993 scopus 로고    scopus 로고
    • RNA structure and the regulation of gene expression
    • Klaff P., Riesner D., Steger G. RNA structure and the regulation of gene expression. Plant Mol. Biol. 1996, 32:89-106.
    • (1996) Plant Mol. Biol. , vol.32 , pp. 89-106
    • Klaff, P.1    Riesner, D.2    Steger, G.3
  • 27
    • 0002681086 scopus 로고
    • Posttranscriptional regulation of gene expression in plants
    • Gallie D.R. Posttranscriptional regulation of gene expression in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1993, 44:77-105.
    • (1993) Annu. Rev. Plant Physiol. Plant Mol. Biol. , vol.44 , pp. 77-105
    • Gallie, D.R.1
  • 28
    • 2542642407 scopus 로고    scopus 로고
    • Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana
    • Kawaguchi R., Girke T., Bray E.A., Bailey-Serres J. Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J. 2004, 38:823-839.
    • (2004) Plant J. , vol.38 , pp. 823-839
    • Kawaguchi, R.1    Girke, T.2    Bray, E.A.3    Bailey-Serres, J.4
  • 29
    • 33745663309 scopus 로고    scopus 로고
    • Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control
    • Nicolai M., et al. Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol. 2006, 141:663-673.
    • (2006) Plant Physiol. , vol.141 , pp. 663-673
    • Nicolai, M.1
  • 30
    • 77949365164 scopus 로고    scopus 로고
    • Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana
    • Matsuura H., Ishibashi Y., Shinmyo A., Kanaya S., Kato K. Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana. Plant Cell Physiol. 2010, 51:448-462.
    • (2010) Plant Cell Physiol. , vol.51 , pp. 448-462
    • Matsuura, H.1    Ishibashi, Y.2    Shinmyo, A.3    Kanaya, S.4    Kato, K.5
  • 31
    • 13944270653 scopus 로고    scopus 로고
    • MRNA sequence features that contribute to translational regulation in Arabidopsis
    • Kawaguchi R., Bailey-Serres J. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res. 2005, 33:955-965.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 955-965
    • Kawaguchi, R.1    Bailey-Serres, J.2
  • 32
    • 77649245858 scopus 로고    scopus 로고
    • Translation efficiency is determined by both codon bias and folding energy
    • Tuller T., Waldman Y.Y., Kupiec M., Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:3645-3650.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 3645-3650
    • Tuller, T.1    Waldman, Y.Y.2    Kupiec, M.3    Ruppin, E.4
  • 33
    • 77649198142 scopus 로고    scopus 로고
    • A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
    • Gu W., Zhou T., Wilke C.O. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comp. Biol. 2010, 6:e1000664.
    • (2010) PLoS Comp. Biol. , vol.6
    • Gu, W.1    Zhou, T.2    Wilke, C.O.3
  • 34
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNAs
    • Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687.
    • (2009) Cell , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 35
    • 0037162702 scopus 로고    scopus 로고
    • Prediction of plant microRNA targets
    • Rhoades M.W., et al. Prediction of plant microRNA targets. Cell 2002, 110:513-520.
    • (2002) Cell , vol.110 , pp. 513-520
    • Rhoades, M.W.1
  • 36
    • 34247258888 scopus 로고    scopus 로고
    • Potent effect of target structure on microRNA function
    • Long D., et al. Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol. 2007, 14:287-294.
    • (2007) Nat. Struct. Mol. Biol. , vol.14 , pp. 287-294
    • Long, D.1
  • 37
    • 22444437609 scopus 로고    scopus 로고
    • Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis
    • Zhao Y., Samal E., Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436:214-220.
    • (2005) Nature , vol.436 , pp. 214-220
    • Zhao, Y.1    Samal, E.2    Srivastava, D.3
  • 38
  • 39
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M., Iovino N., Unnerstall U., Gaul U., Segal E. The role of site accessibility in microRNA target recognition. Nat. Genet. 2007, 39:1278-1284.
    • (2007) Nat. Genet. , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 40
    • 84866952755 scopus 로고    scopus 로고
    • Selection on synonymous sites for increased accessibility around miRNA binding sites in plants
    • Gu W., Wang X., Zhai C., Xie X., Zhou T. Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Mol. Biol. Evol. 2012, 29:3037-3044.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 3037-3044
    • Gu, W.1    Wang, X.2    Zhai, C.3    Xie, X.4    Zhou, T.5
  • 41
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981, 9:133-148.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 42
    • 79955379930 scopus 로고    scopus 로고
    • Vive la difference: biogenesis and evolution of microRNAs in plants and animals
    • Axtell M.J., Westholm J.O., Lai E.C. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 2011, 12:221.
    • (2011) Genome Biol. , vol.12 , pp. 221
    • Axtell, M.J.1    Westholm, J.O.2    Lai, E.C.3
  • 43
    • 45849122499 scopus 로고    scopus 로고
    • Widespread translational inhibition by plant miRNAs and siRNAs
    • Brodersen P., et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008, 320:1185-1190.
    • (2008) Science , vol.320 , pp. 1185-1190
    • Brodersen, P.1
  • 44
    • 68949115601 scopus 로고    scopus 로고
    • Biochemical evidence for translational repression by Arabidopsis microRNAs
    • Lanet E., et al. Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 2009, 21:1762-1768.
    • (2009) Plant Cell , vol.21 , pp. 1762-1768
    • Lanet, E.1
  • 45
    • 78049445573 scopus 로고    scopus 로고
    • Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
    • Zheng Q., et al. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 2010, 6:e1001141.
    • (2010) PLoS Genet. , vol.6
    • Zheng, Q.1
  • 46
    • 77956306662 scopus 로고    scopus 로고
    • Genome-wide measurement of RNA secondary structure in yeast
    • Kertesz M., et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107.
    • (2010) Nature , vol.467 , pp. 103-107
    • Kertesz, M.1
  • 47
    • 78649690492 scopus 로고    scopus 로고
    • FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
    • Underwood J.G., et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods 2010, 7:995-1001.
    • (2010) Nat. Methods , vol.7 , pp. 995-1001
    • Underwood, J.G.1
  • 48
    • 79960571755 scopus 로고    scopus 로고
    • Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
    • Lucks J.B., et al. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc. Natl. Acad. Sci. U.S.A. 2011, 108:11063-11068.
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 11063-11068
    • Lucks, J.B.1
  • 49
    • 33646838978 scopus 로고    scopus 로고
    • A periodic pattern of mRNA secondary structure created by the genetic code
    • Shabalina S.A., Ogurtsov A.Y., Spiridonov N.A. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res. 2006, 34:2428-2437.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2428-2437
    • Shabalina, S.A.1    Ogurtsov, A.Y.2    Spiridonov, N.A.3
  • 50
    • 0036464536 scopus 로고    scopus 로고
    • Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana
    • Lorkovic Z.J., Barta A. Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Res. 2002, 30:623-635.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 623-635
    • Lorkovic, Z.J.1    Barta, A.2
  • 51
    • 63549135467 scopus 로고    scopus 로고
    • Role of plant RNA-binding proteins in development, stress response and genome organization
    • Lorkovic Z.J. Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 2009, 14:229-236.
    • (2009) Trends Plant Sci. , vol.14 , pp. 229-236
    • Lorkovic, Z.J.1
  • 52
    • 82155162650 scopus 로고    scopus 로고
    • Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints
    • Ambrosone A., Costa A., Leone A., Grillo S. Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints. Plant Sci. 2012, 182:12-18.
    • (2012) Plant Sci. , vol.182 , pp. 12-18
    • Ambrosone, A.1    Costa, A.2    Leone, A.3    Grillo, S.4
  • 54
    • 19944413670 scopus 로고    scopus 로고
    • Glycine-rich proteins: a class of novel proteins
    • Mousavi A., Hotta Y. Glycine-rich proteins: a class of novel proteins. Appl. Biochem. Biotechnol. 2005, 120:169-174.
    • (2005) Appl. Biochem. Biotechnol. , vol.120 , pp. 169-174
    • Mousavi, A.1    Hotta, Y.2
  • 55
    • 0034710226 scopus 로고    scopus 로고
    • The Drosophila melanogaster genome: translation factors and RNA binding proteins
    • Lasko P. The Drosophila melanogaster genome: translation factors and RNA binding proteins. J. Cell Biol. 2000, 150:F51-F56.
    • (2000) J. Cell Biol. , vol.150
    • Lasko, P.1
  • 56
    • 80053581878 scopus 로고    scopus 로고
    • RNA-binding proteins
    • WormBook, ed. The C. elegans Research Community
    • M.-H. Lee, T. Schedl, RNA-binding proteins, in: WormBook, ed. The C. elegans Research Community, 2006,. http://www.wormbook.org/.
    • (2006)
    • Lee, M.-H.1    Schedl, T.2
  • 57
    • 84861997955 scopus 로고    scopus 로고
    • The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
    • Baltz A.G., et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 2012, 46:674-690.
    • (2012) Mol. Cell , vol.46 , pp. 674-690
    • Baltz, A.G.1
  • 58
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • Keene J.D., Tenenbaum S.A. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 2002, 9:1161-1167.
    • (2002) Mol. Cell , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 59
    • 0022520577 scopus 로고
    • Heterogeneous nuclear ribonucleoproteins: role in RNA splicing
    • Choi Y.D., Grabowski P.J., Sharp P.A., Dreyfuss G. Heterogeneous nuclear ribonucleoproteins: role in RNA splicing. Science 1986, 231:1534-1539.
    • (1986) Science , vol.231 , pp. 1534-1539
    • Choi, Y.D.1    Grabowski, P.J.2    Sharp, P.A.3    Dreyfuss, G.4
  • 60
    • 0026716104 scopus 로고
    • SR proteins: a conserved family of pre-mRNA splicing factors
    • Zahler A.M., Lane W.S., Stolk J.A., Roth M.B. SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 1992, 6:837-847.
    • (1992) Genes Dev. , vol.6 , pp. 837-847
    • Zahler, A.M.1    Lane, W.S.2    Stolk, J.A.3    Roth, M.B.4
  • 61
    • 0037266853 scopus 로고    scopus 로고
    • The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA
    • Staiger D., Zecca L., Wieczorek Kirk D.A., Apel K., Eckstein L. The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J. 2003, 33:361-371.
    • (2003) Plant J. , vol.33 , pp. 361-371
    • Staiger, D.1    Zecca, L.2    Wieczorek Kirk, D.A.3    Apel, K.4    Eckstein, L.5
  • 62
    • 0033561378 scopus 로고    scopus 로고
    • AtSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes
    • Lopato S., et al. atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes. Genes Dev. 1999, 13:987-1001.
    • (1999) Genes Dev. , vol.13 , pp. 987-1001
    • Lopato, S.1
  • 63
    • 0036264995 scopus 로고    scopus 로고
    • UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants
    • Lambermon M.H., et al. UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants. Mol. Cell. Biol. 2002, 22:4346-4357.
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 4346-4357
    • Lambermon, M.H.1
  • 64
    • 77954408142 scopus 로고    scopus 로고
    • The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis
    • dit Frey N.F., et al. The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis. Plant Cell 2010, 22:1575-1591.
    • (2010) Plant Cell , vol.22 , pp. 1575-1591
    • dit Frey, N.F.1
  • 65
    • 51249095587 scopus 로고    scopus 로고
    • Overexpression of wound-responsive RNA-binding proteins induces leaf senescence and hypersensitive-like cell death
    • Kim C.Y., Bove J., Assmann S.M. Overexpression of wound-responsive RNA-binding proteins induces leaf senescence and hypersensitive-like cell death. New Phytol. 2008, 180:57-70.
    • (2008) New Phytol. , vol.180 , pp. 57-70
    • Kim, C.Y.1    Bove, J.2    Assmann, S.M.3
  • 66
    • 0037102432 scopus 로고    scopus 로고
    • Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase
    • Li J., et al. Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase. Nature 2002, 418:793-797.
    • (2002) Nature , vol.418 , pp. 793-797
    • Li, J.1
  • 67
    • 80053318065 scopus 로고    scopus 로고
    • RNA-based regulation in the plant circadian clock
    • Staiger D., Green R. RNA-based regulation in the plant circadian clock. Trends Plant Sci. 2011, 16:517-523.
    • (2011) Trends Plant Sci. , vol.16 , pp. 517-523
    • Staiger, D.1    Green, R.2
  • 68
    • 57449111072 scopus 로고    scopus 로고
    • Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana
    • Branco-Price C., Kaiser K.A., Jang C.J., Larive C.K., Bailey-Serres J. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 2008, 56:743-755.
    • (2008) Plant J. , vol.56 , pp. 743-755
    • Branco-Price, C.1    Kaiser, K.A.2    Jang, C.J.3    Larive, C.K.4    Bailey-Serres, J.5
  • 69
    • 84863641060 scopus 로고    scopus 로고
    • Post-transcriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice
    • Park S.H., et al. Post-transcriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice. Plant Physiol. 2012, 159:1111-1124.
    • (2012) Plant Physiol. , vol.159 , pp. 1111-1124
    • Park, S.H.1
  • 70
    • 34249064705 scopus 로고    scopus 로고
    • A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity
    • Fu Z.Q., et al. A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity. Nature 2007, 447:284-288.
    • (2007) Nature , vol.447 , pp. 284-288
    • Fu, Z.Q.1
  • 71
    • 83355169694 scopus 로고    scopus 로고
    • Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity
    • Jeong B.R., et al. Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity. J. Biol. Chem. 2011, 286:43272-43281.
    • (2011) J. Biol. Chem. , vol.286 , pp. 43272-43281
    • Jeong, B.R.1
  • 72
    • 33845420384 scopus 로고    scopus 로고
    • A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress
    • Dong C.H., et al. A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress. Mol. Cell. Biol. 2006, 26:9533-9543.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 9533-9543
    • Dong, C.H.1
  • 73
    • 77953009768 scopus 로고    scopus 로고
    • Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process
    • Kim J.Y., et al. Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process. J. Exp. Bot. 2010, 61:2317-2325.
    • (2010) J. Exp. Bot. , vol.61 , pp. 2317-2325
    • Kim, J.Y.1
  • 74
    • 33745765847 scopus 로고    scopus 로고
    • STABILIZED1 a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis
    • Lee B.H., Kapoor A., Zhu J., Zhu J.K. STABILIZED1 a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis. Plant Cell 2006, 18:1736-1749.
    • (2006) Plant Cell , vol.18 , pp. 1736-1749
    • Lee, B.H.1    Kapoor, A.2    Zhu, J.3    Zhu, J.K.4
  • 75
    • 33745930546 scopus 로고    scopus 로고
    • Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid
    • Riera M., Redko Y., Leung J. Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid. FEBS Lett. 2006, 580:4160-4165.
    • (2006) FEBS Lett. , vol.580 , pp. 4160-4165
    • Riera, M.1    Redko, Y.2    Leung, J.3
  • 76
    • 0035654544 scopus 로고    scopus 로고
    • Modulation of abscisic acid signal transduction and biosynthesis by an Sm-like protein in Arabidopsis
    • Xiong L., et al. Modulation of abscisic acid signal transduction and biosynthesis by an Sm-like protein in Arabidopsis. Dev. Cell 2001, 1:771-781.
    • (2001) Dev. Cell , vol.1 , pp. 771-781
    • Xiong, L.1
  • 77
    • 42949109848 scopus 로고    scopus 로고
    • The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1
    • Michlewski G., Sanford J.R., Caceres J.F. The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol. Cell 2008, 30:179-189.
    • (2008) Mol. Cell , vol.30 , pp. 179-189
    • Michlewski, G.1    Sanford, J.R.2    Caceres, J.F.3
  • 78
    • 77950357450 scopus 로고    scopus 로고
    • A splicing-independent function of SF2/ASF in microRNA processing
    • Wu H., et al. A splicing-independent function of SF2/ASF in microRNA processing. Mol. Cell 2010, 38:67-77.
    • (2010) Mol. Cell , vol.38 , pp. 67-77
    • Wu, H.1
  • 79
    • 58749102066 scopus 로고    scopus 로고
    • Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis
    • Schoning J.C., Streitner C., Meyer I.M., Gao Y., Staiger D. Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Res. 2008, 36:6977-6987.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6977-6987
    • Schoning, J.C.1    Streitner, C.2    Meyer, I.M.3    Gao, Y.4    Staiger, D.5
  • 80
    • 78649550144 scopus 로고    scopus 로고
    • Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control
    • Stauffer E., Westermann A., Wagner G., Wachter A. Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control. Plant J. 2010, 64:243-255.
    • (2010) Plant J. , vol.64 , pp. 243-255
    • Stauffer, E.1    Westermann, A.2    Wagner, G.3    Wachter, A.4
  • 81
    • 54949148332 scopus 로고    scopus 로고
    • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    • Hogan D.J., Riordan D.P., Gerber A.P., Herschlag D., Brown P.O. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 2008, 6:e255.
    • (2008) PLoS Biol. , vol.6
    • Hogan, D.J.1    Riordan, D.P.2    Gerber, A.P.3    Herschlag, D.4    Brown, P.O.5
  • 82
    • 73949131510 scopus 로고    scopus 로고
    • Genome-wide analysis of RNA-protein interactions in plants
    • Barkan A. Genome-wide analysis of RNA-protein interactions in plants. Methods Mol. Biol. 2009, 553:13-37.
    • (2009) Methods Mol. Biol. , vol.553 , pp. 13-37
    • Barkan, A.1
  • 83
    • 84871195123 scopus 로고    scopus 로고
    • An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana
    • Streitner C., Koster T., Simpson C.G., Shaw P., Danisman S., Brown J.W., Staiger D. An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res. 2012, 40:11240-11255.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 11240-11255
    • Streitner, C.1    Koster, T.2    Simpson, C.G.3    Shaw, P.4    Danisman, S.5    Brown, J.W.6    Staiger, D.7
  • 84
    • 77952546929 scopus 로고    scopus 로고
    • Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds
    • Crofts A.J., Crofts N., Whitelegge J.P., Okita T.W. Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds. Planta 2010, 231:1261-1276.
    • (2010) Planta , vol.231 , pp. 1261-1276
    • Crofts, A.J.1    Crofts, N.2    Whitelegge, J.P.3    Okita, T.W.4
  • 85
    • 27944508215 scopus 로고    scopus 로고
    • CLIP: a method for identifying protein-RNA interaction sites in living cells
    • Ule J., Jensen K., Mele A., Darnell R.B. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 2005, 37:376-386.
    • (2005) Methods , vol.37 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 86
    • 84870026823 scopus 로고    scopus 로고
    • Genome-wide identification of miRNA targets by PAR-CLIP
    • Hafner M., Lianoglou S., Tuschl T., Betel D. Genome-wide identification of miRNA targets by PAR-CLIP. Methods 2012, 58:94-105.
    • (2012) Methods , vol.58 , pp. 94-105
    • Hafner, M.1    Lianoglou, S.2    Tuschl, T.3    Betel, D.4
  • 87
    • 80455179726 scopus 로고    scopus 로고
    • ICLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution
    • Konig J., et al. iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J. Vis. Exp. 2011, 30:2638.
    • (2011) J. Vis. Exp. , vol.30 , pp. 2638
    • Konig, J.1
  • 88
    • 0242497663 scopus 로고    scopus 로고
    • CLIP identifies Nova-regulated RNA networks in the brain
    • Ule J., et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003, 302:1212-1215.
    • (2003) Science , vol.302 , pp. 1212-1215
    • Ule, J.1
  • 89
    • 84861161751 scopus 로고    scopus 로고
    • Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
    • Huelga S.C., et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012, 1:167-178.
    • (2012) Cell Rep. , vol.1 , pp. 167-178
    • Huelga, S.C.1
  • 90
    • 61849139645 scopus 로고    scopus 로고
    • Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    • Sanford J.R., et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 2009, 19:381-394.
    • (2009) Genome Res. , vol.19 , pp. 381-394
    • Sanford, J.R.1
  • 91
    • 79960779323 scopus 로고    scopus 로고
    • FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism
    • Darnell J.C., et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 2011, 146:247-261.
    • (2011) Cell , vol.146 , pp. 247-261
    • Darnell, J.C.1
  • 92
    • 16544392851 scopus 로고    scopus 로고
    • Crosslinking of ribosomal proteins to RNA in maize ribosomes by UV-B and its effects on translation
    • Casati P., Walbot V. Crosslinking of ribosomal proteins to RNA in maize ribosomes by UV-B and its effects on translation. Plant Physiol. 2004, 136:3319-3332.
    • (2004) Plant Physiol. , vol.136 , pp. 3319-3332
    • Casati, P.1    Walbot, V.2
  • 93
    • 0033740021 scopus 로고    scopus 로고
    • RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells
    • Lorkovic Z.J., Wieczorek Kirk D.A., Klahre U., Hemmings-Mieszczak M., Filipowicz W. RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells. RNA 2000, 6:1610-1624.
    • (2000) RNA , vol.6 , pp. 1610-1624
    • Lorkovic, Z.J.1    Wieczorek Kirk, D.A.2    Klahre, U.3    Hemmings-Mieszczak, M.4    Filipowicz, W.5
  • 95
    • 77950903733 scopus 로고    scopus 로고
    • A proteomic analysis of oligo(dT)-bound mRNP containing oxidative stress-induced Arabidopsis thaliana RNA-binding proteins ATGRP7 and ATGRP8
    • Schmidt F., et al. A proteomic analysis of oligo(dT)-bound mRNP containing oxidative stress-induced Arabidopsis thaliana RNA-binding proteins ATGRP7 and ATGRP8. Mol. Biol. Rep. 2010, 37:839-845.
    • (2010) Mol. Biol. Rep. , vol.37 , pp. 839-845
    • Schmidt, F.1
  • 96
    • 37749036789 scopus 로고    scopus 로고
    • Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles
    • Delannoy E., Stanley W.A., Bond C.S., Small I.D. Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles. Biochem. Soc. Trans. 2007, 35:1643-1647.
    • (2007) Biochem. Soc. Trans. , vol.35 , pp. 1643-1647
    • Delannoy, E.1    Stanley, W.A.2    Bond, C.S.3    Small, I.D.4
  • 97
    • 44649133995 scopus 로고    scopus 로고
    • On the expansion of the pentatricopeptide repeat gene family in plants
    • O'Toole N., et al. On the expansion of the pentatricopeptide repeat gene family in plants. Mol. Biol. Evol. 2008, 25:1120-1128.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1120-1128
    • O'Toole, N.1
  • 98
    • 0026740718 scopus 로고
    • Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box
    • Kiledjian M., Dreyfuss G. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J. 1992, 11:2655-2664.
    • (1992) EMBO J. , vol.11 , pp. 2655-2664
    • Kiledjian, M.1    Dreyfuss, G.2
  • 99
    • 0028129989 scopus 로고
    • Conserved structures and diversity of functions of RNA-binding proteins
    • Burd C.G., Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science 1994, 265:615-621.
    • (1994) Science , vol.265 , pp. 615-621
    • Burd, C.G.1    Dreyfuss, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.