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Volumn 1, Issue 5, 2012, Pages 570-581

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

Author keywords

[No Author keywords available]

Indexed keywords

PUMILIO AND FBF PROTEIN; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

EID: 84861705421     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2012.04.003     Document Type: Article
Times cited : (95)

References (55)
  • 1
    • 58649114059 scopus 로고    scopus 로고
    • C. elegans RNA-binding proteins PUF-8 and MEX-3 function redundantly to promote germline stem cell mitosis
    • Ariz M., Mainpal R., Subramaniam K. C. elegans RNA-binding proteins PUF-8 and MEX-3 function redundantly to promote germline stem cell mitosis. Dev. Biol. 2009, 326:295-304.
    • (2009) Dev. Biol. , vol.326 , pp. 295-304
    • Ariz, M.1    Mainpal, R.2    Subramaniam, K.3
  • 2
    • 33747823564 scopus 로고    scopus 로고
    • MEME: discovering and analyzing DNA and protein sequence motifs
    • Web Server issue
    • Bailey T.L., Williams N., Misleh C., Li W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34(Web Server issue):W369-W373.
    • (2006) Nucleic Acids Res. , vol.34
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 3
    • 0036168937 scopus 로고    scopus 로고
    • Engineering polydactyl zinc-finger transcription factors
    • Beerli R.R., Barbas C.F. Engineering polydactyl zinc-finger transcription factors. Nat. Biotechnol. 2002, 20:135-141.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 135-141
    • Beerli, R.R.1    Barbas, C.F.2
  • 4
    • 15444365620 scopus 로고    scopus 로고
    • Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1
    • Bernstein D., Hook B., Hajarnavis A., Opperman L., Wickens M. Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1. RNA 2005, 11:447-458.
    • (2005) RNA , vol.11 , pp. 447-458
    • Bernstein, D.1    Hook, B.2    Hajarnavis, A.3    Opperman, L.4    Wickens, M.5
  • 5
    • 56749096054 scopus 로고    scopus 로고
    • Translational control of localized mRNAs: restricting protein synthesis in space and time
    • Besse F., Ephrussi A. Translational control of localized mRNAs: restricting protein synthesis in space and time. Nat. Rev. Mol. Cell Biol. 2008, 9:971-980.
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 971-980
    • Besse, F.1    Ephrussi, A.2
  • 6
    • 58049213723 scopus 로고    scopus 로고
    • CPEB regulation of human cellular senescence, energy metabolism, and p53 mRNA translation
    • Burns D.M., Richter J.D. CPEB regulation of human cellular senescence, energy metabolism, and p53 mRNA translation. Genes Dev. 2008, 22:3449-3460.
    • (2008) Genes Dev. , vol.22 , pp. 3449-3460
    • Burns, D.M.1    Richter, J.D.2
  • 9
    • 77952703757 scopus 로고    scopus 로고
    • Translational repression by PUF proteins in vitro
    • Chritton J.J., Wickens M. Translational repression by PUF proteins in vitro. RNA 2010, 16:1217-1225.
    • (2010) RNA , vol.16 , pp. 1217-1225
    • Chritton, J.J.1    Wickens, M.2
  • 11
    • 80053159210 scopus 로고    scopus 로고
    • Targeted translational regulation using the PUF protein family scaffold
    • Cooke A., Prigge A., Opperman L., Wickens M. Targeted translational regulation using the PUF protein family scaffold. Proc. Natl. Acad. Sci. USA 2011, 108:15870-15875.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 15870-15875
    • Cooke, A.1    Prigge, A.2    Opperman, L.3    Wickens, M.4
  • 14
    • 0035917508 scopus 로고    scopus 로고
    • Structure of Pumilio reveals similarity between RNA and peptide binding motifs
    • Edwards T.A., Pyle S.E., Wharton R.P., Aggarwal A.K. Structure of Pumilio reveals similarity between RNA and peptide binding motifs. Cell 2001, 105:281-289.
    • (2001) Cell , vol.105 , pp. 281-289
    • Edwards, T.A.1    Pyle, S.E.2    Wharton, R.P.3    Aggarwal, A.K.4
  • 15
    • 0142123289 scopus 로고    scopus 로고
    • Model of the brain tumor-Pumilio translation repressor complex
    • Edwards T.A., Wilkinson B.D., Wharton R.P., Aggarwal A.K. Model of the brain tumor-Pumilio translation repressor complex. Genes Dev. 2003, 17:2508-2513.
    • (2003) Genes Dev. , vol.17 , pp. 2508-2513
    • Edwards, T.A.1    Wilkinson, B.D.2    Wharton, R.P.3    Aggarwal, A.K.4
  • 16
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 17
    • 0031576995 scopus 로고    scopus 로고
    • Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site
    • Frank D.E., Saecker R.M., Bond J.P., Capp M.W., Tsodikov O.V., Melcher S.E., Levandoski M.M., Record M.T. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. J. Mol. Biol. 1997, 267:1186-1206.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1186-1206
    • Frank, D.E.1    Saecker, R.M.2    Bond, J.P.3    Capp, M.W.4    Tsodikov, O.V.5    Melcher, S.E.6    Levandoski, M.M.7    Record, M.T.8
  • 18
    • 52349122355 scopus 로고    scopus 로고
    • Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
    • Galgano A., Forrer M., Jaskiewicz L., Kanitz A., Zavolan M., Gerber A.P. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One 2008, 3:e3164.
    • (2008) PLoS One , vol.3
    • Galgano, A.1    Forrer, M.2    Jaskiewicz, L.3    Kanitz, A.4    Zavolan, M.5    Gerber, A.P.6
  • 19
    • 0035697276 scopus 로고    scopus 로고
    • Structural studies of Ets-1/Pax5 complex formation on DNA
    • Garvie C.W., Hagman J., Wolberger C. Structural studies of Ets-1/Pax5 complex formation on DNA. Mol. Cell 2001, 8:1267-1276.
    • (2001) Mol. Cell , vol.8 , pp. 1267-1276
    • Garvie, C.W.1    Hagman, J.2    Wolberger, C.3
  • 20
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • Gerber A.P., Herschlag D., Brown P.O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2004, 2:E79.
    • (2004) PLoS Biol. , vol.2
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 21
    • 33645217973 scopus 로고    scopus 로고
    • Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
    • Gerber A.P., Luschnig S., Krasnow M.A., Brown P.O., Herschlag D. Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 2006, 103:4487-4492.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 4487-4492
    • Gerber, A.P.1    Luschnig, S.2    Krasnow, M.A.3    Brown, P.O.4    Herschlag, D.5
  • 22
  • 24
    • 0031883566 scopus 로고    scopus 로고
    • Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zinc finger
    • Hake L.E., Mendez R., Richter J.D. Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zinc finger. Mol. Cell. Biol. 1998, 18:685-693.
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 685-693
    • Hake, L.E.1    Mendez, R.2    Richter, J.D.3
  • 25
    • 34447503943 scopus 로고    scopus 로고
    • Two yeast PUF proteins negatively regulate a single mRNA
    • Hook B.A., Goldstrohm A.C., Seay D.J., Wickens M. Two yeast PUF proteins negatively regulate a single mRNA. J. Biol. Chem. 2007, 282:15430-15438.
    • (2007) J. Biol. Chem. , vol.282 , pp. 15430-15438
    • Hook, B.A.1    Goldstrohm, A.C.2    Seay, D.J.3    Wickens, M.4
  • 26
    • 27144544947 scopus 로고    scopus 로고
    • Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay
    • Houshmandi S.S., Olivas W.M. Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay. RNA 2005, 11:1655-1666.
    • (2005) RNA , vol.11 , pp. 1655-1666
    • Houshmandi, S.S.1    Olivas, W.M.2
  • 28
    • 77649264236 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator
    • Kershner A.M., Kimble J. Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator. Proc. Natl. Acad. Sci. USA 2010, 107:3936-3941.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 3936-3941
    • Kershner, A.M.1    Kimble, J.2
  • 29
    • 66449119611 scopus 로고    scopus 로고
    • A single C. elegans PUF protein binds RNA in multiple modes
    • Koh Y.Y., Opperman L., Stumpf C., Mandan A., Keles S., Wickens M. A single C. elegans PUF protein binds RNA in multiple modes. RNA 2009, 15:1090-1099.
    • (2009) RNA , vol.15 , pp. 1090-1099
    • Koh, Y.Y.1    Opperman, L.2    Stumpf, C.3    Mandan, A.4    Keles, S.5    Wickens, M.6
  • 30
    • 79954510568 scopus 로고    scopus 로고
    • Diverse roles of host RNA binding proteins in RNA virus replication
    • Li Z., Nagy P.D. Diverse roles of host RNA binding proteins in RNA virus replication. RNA Biol. 2011, 8:305-315.
    • (2011) RNA Biol. , vol.8 , pp. 305-315
    • Li, Z.1    Nagy, P.D.2
  • 32
    • 41649092045 scopus 로고    scopus 로고
    • Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p
    • Miller M.T., Higgin J.J., Hall T.M. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nat. Struct. Mol. Biol. 2008, 15:397-402.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 397-402
    • Miller, M.T.1    Higgin, J.J.2    Hall, T.M.3
  • 33
    • 44949255018 scopus 로고    scopus 로고
    • Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
    • Morris A.R., Mukherjee N., Keene J.D. Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol. Cell. Biol. 2008, 28:4093-4103.
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 4093-4103
    • Morris, A.R.1    Mukherjee, N.2    Keene, J.D.3
  • 35
    • 33644991514 scopus 로고    scopus 로고
    • A single spacer nucleotide determines the specificities of two mRNA regulatory proteins
    • Opperman L., Hook B., DeFino M., Bernstein D.S., Wickens M. A single spacer nucleotide determines the specificities of two mRNA regulatory proteins. Nat. Struct. Mol. Biol. 2005, 12:945-951.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 945-951
    • Opperman, L.1    Hook, B.2    DeFino, M.3    Bernstein, D.S.4    Wickens, M.5
  • 37
    • 84863116797 scopus 로고    scopus 로고
    • Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket
    • Qiu C., Kershner A., Wang Y., Holley C.P., Wilinski D., Keles S., Kimble J., Wickens M., Hall T.M. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket. J. Biol. Chem. 2012, 287:6949-6957.
    • (2012) J. Biol. Chem. , vol.287 , pp. 6949-6957
    • Qiu, C.1    Kershner, A.2    Wang, Y.3    Holley, C.P.4    Wilinski, D.5    Keles, S.6    Kimble, J.7    Wickens, M.8    Hall, T.M.9
  • 39
    • 34249908103 scopus 로고    scopus 로고
    • CPEB: a life in translation
    • Richter J.D. CPEB: a life in translation. Trends Biochem. Sci. 2007, 32:279-285.
    • (2007) Trends Biochem. Sci. , vol.32 , pp. 279-285
    • Richter, J.D.1
  • 42
    • 49349088194 scopus 로고    scopus 로고
    • Translational control in early development: CPEB, P-bodies and germinal granules
    • Standart N., Minshall N. Translational control in early development: CPEB, P-bodies and germinal granules. Biochem. Soc. Trans. 2008, 36:671-676.
    • (2008) Biochem. Soc. Trans. , vol.36 , pp. 671-676
    • Standart, N.1    Minshall, N.2
  • 43
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • Stormo G.D., Zhao Y. Determining the specificity of protein-DNA interactions. Nat. Rev. Genet. 2010, 11:751-760.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 45
  • 46
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriphage T4 DNA polymerase
    • Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriphage T4 DNA polymerase. Science 1990, 249:505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 47
    • 32344440041 scopus 로고    scopus 로고
    • RNA binding proteins and the regulation of neuronal synaptic plasticity
    • Ule J., Darnell R.B. RNA binding proteins and the regulation of neuronal synaptic plasticity. Curr. Opin. Neurobiol. 2006, 16:102-110.
    • (2006) Curr. Opin. Neurobiol. , vol.16 , pp. 102-110
    • Ule, J.1    Darnell, R.B.2
  • 48
    • 0035022798 scopus 로고    scopus 로고
    • Crystal structure of a Pumilio homology domain
    • Wang X., Zamore P.D., Hall T.M. Crystal structure of a Pumilio homology domain. Mol. Cell 2001, 7:855-865.
    • (2001) Mol. Cell , vol.7 , pp. 855-865
    • Wang, X.1    Zamore, P.D.2    Hall, T.M.3
  • 49
    • 0037162703 scopus 로고    scopus 로고
    • Modular recognition of RNA by a human pumilio-homology domain
    • Wang X., McLachlan J., Zamore P.D., Hall T.M. Modular recognition of RNA by a human pumilio-homology domain. Cell 2002, 110:501-512.
    • (2002) Cell , vol.110 , pp. 501-512
    • Wang, X.1    McLachlan, J.2    Zamore, P.D.3    Hall, T.M.4
  • 50
    • 70350719211 scopus 로고    scopus 로고
    • Engineering splicing factors with designed specificities
    • Wang Y., Cheong C.G., Hall T.M., Wang Z. Engineering splicing factors with designed specificities. Nat. Methods 2009, 6:825-830.
    • (2009) Nat. Methods , vol.6 , pp. 825-830
    • Wang, Y.1    Cheong, C.G.2    Hall, T.M.3    Wang, Z.4
  • 51
    • 73949159967 scopus 로고    scopus 로고
    • Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein
    • Wang Y., Opperman L., Wickens M., Hall T.M. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein. Proc. Natl. Acad. Sci. USA 2009, 106:20186-20191.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 20186-20191
    • Wang, Y.1    Opperman, L.2    Wickens, M.3    Hall, T.M.4
  • 52
    • 0002068909 scopus 로고    scopus 로고
    • Translational control of developmental decisions
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, N. Sonenberg, J.W.B. Hershey, M. Mathews (Eds.)
    • Wickens M., Goodwin E.B., Kimble J., Strickland S., Hentze M. Translational control of developmental decisions. Translational Control of Gene Expression 2000, 295-370. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Second Edition. N. Sonenberg, J.W.B. Hershey, M. Mathews (Eds.).
    • (2000) Translational Control of Gene Expression , pp. 295-370
    • Wickens, M.1    Goodwin, E.B.2    Kimble, J.3    Strickland, S.4    Hentze, M.5
  • 53
    • 0030757678 scopus 로고    scopus 로고
    • Nanos and pumilio establish embryonic polarity in Drosophila by promoting posterior deadenylation of hunchback mRNA
    • Wreden C., Verrotti A.C., Schisa J.A., Lieberfarb M.E., Strickland S. Nanos and pumilio establish embryonic polarity in Drosophila by promoting posterior deadenylation of hunchback mRNA. Development 1997, 124:3015-3023.
    • (1997) Development , vol.124 , pp. 3015-3023
    • Wreden, C.1    Verrotti, A.C.2    Schisa, J.A.3    Lieberfarb, M.E.4    Strickland, S.5
  • 54
    • 0031452082 scopus 로고    scopus 로고
    • A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line
    • Zhang B., Gallegos M., Puoti A., Durkin E., Fields S., Kimble J., Wickens M.P. A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature 1997, 390:477-484.
    • (1997) Nature , vol.390 , pp. 477-484
    • Zhang, B.1    Gallegos, M.2    Puoti, A.3    Durkin, E.4    Fields, S.5    Kimble, J.6    Wickens, M.P.7
  • 55
    • 73949084779 scopus 로고    scopus 로고
    • A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs
    • Zhu D., Stumpf C.R., Krahn J.M., Wickens M., Hall T.M. A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs. Proc. Natl. Acad. Sci. USA 2009, 106:20192-20197.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 20192-20197
    • Zhu, D.1    Stumpf, C.R.2    Krahn, J.M.3    Wickens, M.4    Hall, T.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.