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Volumn 588, Issue 20, 2014, Pages 3649-3664

Ribonomic approaches to study the RNA-binding proteome

Author keywords

Non coding; Ribonome; Ribonucleoprotein particles (RNPs); RNA binding proteins (RBPs); RNA centric methods; RNA protein interactions; RNAs (ncRNAs)

Indexed keywords

BIOTIN; COAT PROTEIN; COMPLEMENTARY RNA; LONG UNTRANSLATED RNA; MESSENGER RNA; PEPTIDE NUCLEIC ACID; PROTEIN CSY4; PROTEIN MS2; PROTEOME; RIBONUCLEASE; RNA BINDING PROTEIN; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG; RNA;

EID: 84907272104     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2014.07.039     Document Type: Review
Times cited : (38)

References (184)
  • 1
    • 0032489021 scopus 로고    scopus 로고
    • Mechanical devices of the spliceosome: Motors, clocks, springs, and things
    • J.P. Staley, and C. Guthrie Mechanical devices of the spliceosome: motors, clocks, springs, and things Cell 92 1998 315 326
    • (1998) Cell , vol.92 , pp. 315-326
    • Staley, J.P.1    Guthrie, C.2
  • 2
    • 60049097909 scopus 로고    scopus 로고
    • The ribonome: A dominant force in co-ordinating gene expression
    • K.D. Mansfield, and J.D. Keene The ribonome: a dominant force in co-ordinating gene expression Biol. Cell 101 2009 169 181
    • (2009) Biol. Cell , vol.101 , pp. 169-181
    • Mansfield, K.D.1    Keene, J.D.2
  • 3
    • 44449166478 scopus 로고    scopus 로고
    • RNA-binding proteins and post-transcriptional gene regulation
    • T. Glisovic, J.L. Bachorik, J. Yong, and G. Dreyfuss RNA-binding proteins and post-transcriptional gene regulation FEBS Lett. 582 2008 1977 1986
    • (2008) FEBS Lett. , vol.582 , pp. 1977-1986
    • Glisovic, T.1    Bachorik, J.L.2    Yong, J.3    Dreyfuss, G.4
  • 4
    • 0037154982 scopus 로고    scopus 로고
    • A unified theory of gene expression
    • G. Orphanides, and D. Reinberg A unified theory of gene expression Cell 108 2002 439 451
    • (2002) Cell , vol.108 , pp. 439-451
    • Orphanides, G.1    Reinberg, D.2
  • 5
    • 0347363472 scopus 로고    scopus 로고
    • Cup-ling oskar RNA localization and translational control
    • P. Lasko Cup-ling oskar RNA localization and translational control J. Cell Biol. 163 2003 1189 1191
    • (2003) J. Cell Biol. , vol.163 , pp. 1189-1191
    • Lasko, P.1
  • 6
    • 0027374048 scopus 로고
    • Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system
    • R.J. Buckanovich, J.B. Posner, and R.B. Darnell Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system Neuron 11 1993 657 672
    • (1993) Neuron , vol.11 , pp. 657-672
    • Buckanovich, R.J.1    Posner, J.B.2    Darnell, R.B.3
  • 7
    • 23944466443 scopus 로고    scopus 로고
    • ADAR gene family and A-to-I RNA editing: Diverse roles in posttranscriptional gene regulation
    • L. Valente, and K. Nishikura ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation Prog. Nucleic Acid Res. Mol. Biol. 79 2005 299 338
    • (2005) Prog. Nucleic Acid Res. Mol. Biol. , vol.79 , pp. 299-338
    • Valente, L.1    Nishikura, K.2
  • 8
    • 1642488290 scopus 로고    scopus 로고
    • Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease
    • K. Ryan, O. Calvo, and J.L. Manley Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease RNA 10 2004 565 573
    • (2004) RNA , vol.10 , pp. 565-573
    • Ryan, K.1    Calvo, O.2    Manley, J.L.3
  • 9
    • 2342523175 scopus 로고    scopus 로고
    • MRNA export: An assembly line from genes to nuclear pores
    • P. Vinciguerra, and F. Stutz MRNA export: an assembly line from genes to nuclear pores Curr. Opin. Cell Biol. 16 2004 285 292
    • (2004) Curr. Opin. Cell Biol. , vol.16 , pp. 285-292
    • Vinciguerra, P.1    Stutz, F.2
  • 10
    • 0034675993 scopus 로고    scopus 로고
    • She2p, a novel RNA-binding protein tethers ASH1 mRNA to the Myo4p myosin motor via She3p
    • F. Bohl, C. Kruse, A. Frank, D. Ferring, and R.P. Jansen She2p, a novel RNA-binding protein tethers ASH1 mRNA to the Myo4p myosin motor via She3p EMBO J. 19 2000 5514 5524
    • (2000) EMBO J. , vol.19 , pp. 5514-5524
    • Bohl, F.1    Kruse, C.2    Frank, A.3    Ferring, D.4    Jansen, R.P.5
  • 11
    • 18344371641 scopus 로고    scopus 로고
    • Moving messages: The intracellular localization of mRNAs
    • D. St Johnsto Moving messages: the intracellular localization of mRNAs Nat. Rev. Mol. Cell Biol. 6 2005 363 375
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 363-375
    • St Johnsto, D.1
  • 12
    • 5044229348 scopus 로고    scopus 로고
    • Molecular mechanisms of translational control
    • F. Gebauer, and M.W. Hentze Molecular mechanisms of translational control Nat. Rev. Mol. Cell Biol. 5 2004 827 835
    • (2004) Nat. Rev. Mol. Cell Biol. , vol.5 , pp. 827-835
    • Gebauer, F.1    Hentze, M.W.2
  • 14
    • 84862883971 scopus 로고    scopus 로고
    • RNA-protein interactions in vivo: Global gets specific
    • M.-L. Änkö, and K.M. Neugebauer RNA-protein interactions in vivo: global gets specific Trends Biochem. Sci. 37 2012 255 262
    • (2012) Trends Biochem. Sci. , vol.37 , pp. 255-262
    • Änkö, M.-L.1    Neugebauer, K.M.2
  • 15
    • 84870330338 scopus 로고    scopus 로고
    • From specific to global analysis of posttranscriptional regulation in eukaryotes: Posttranscriptional regulatory networks
    • S.C. Janga From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks Brief Funct. Genomic 11 6 2012 505 521
    • (2012) Brief Funct. Genomic , vol.11 , Issue.6 , pp. 505-521
    • Janga, S.C.1
  • 16
    • 84892999996 scopus 로고    scopus 로고
    • Methods for comprehensive experimental identification of RNA-protein interactions
    • C.A. McHugh, P. Russell, and M. Guttman Methods for comprehensive experimental identification of RNA-protein interactions Genome Biol. 15 203 2014 10.1186/gb4152
    • (2014) Genome Biol. , vol.15 , Issue.203
    • McHugh, C.A.1    Russell, P.2    Guttman, M.3
  • 17
    • 84907264121 scopus 로고    scopus 로고
    • The RBPome: Where the brains meet the brawn
    • N. Attar The RBPome: where the brains meet the brawn Genome Biol. 15 402 2014 10.1186/gb4153
    • (2014) Genome Biol. , vol.15 , Issue.402
    • Attar, N.1
  • 19
    • 84892402537 scopus 로고    scopus 로고
    • Dissecting the expression landscape of RNA-binding proteins in human cancer
    • B. Kechavarzi, and S.C. Janga Dissecting the expression landscape of RNA-binding proteins in human cancer Genome Biol. 15 R14 2014 1 16
    • (2014) Genome Biol. , vol.15 , Issue.R14 , pp. 1-16
    • Kechavarzi, B.1    Janga, S.C.2
  • 20
    • 79961091137 scopus 로고    scopus 로고
    • Evolution of RNA-binding proteins in animals: Insights from genome-wide analysis in the sponge Amphimedon queenslandica
    • P. Kerner, S.M. Degnan, L. Marchand, B.M. Degnan, and M. Vervoort Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica Mol. Biol. Evol. 28 2011 2289 2303
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2289-2303
    • Kerner, P.1    Degnan, S.M.2    Marchand, L.3    Degnan, B.M.4    Vervoort, M.5
  • 21
    • 0036529621 scopus 로고    scopus 로고
    • Comparative genomics and evolution of proteins involved in RNA metabolism
    • V. Anantharaman, E.V. Koonin, and L. Aravind Comparative genomics and evolution of proteins involved in RNA metabolism Nucleic Acids Res. 30 7 2002 1427 1464
    • (2002) Nucleic Acids Res. , vol.30 , Issue.7 , pp. 1427-1464
    • Anantharaman, V.1    Koonin, E.V.2    Aravind, L.3
  • 22
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • J.D. Keene, and S.A. Tenenbaum Eukaryotic mRNPs may represent posttranscriptional operons Mol. Cell 9 2002 1161 1167
    • (2002) Mol. Cell , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 23
    • 84883151591 scopus 로고    scopus 로고
    • A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels
    • A.M. Tamburino, S.P. Ryder, and A.J.M. Walhout A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels G3 - Genes Genom. Genet. 3 2 2013 297 304
    • (2013) G3 - Genes Genom. Genet. , vol.3 , Issue.2 , pp. 297-304
    • Tamburino, A.M.1    Ryder, S.P.2    Walhout, A.J.M.3
  • 24
    • 54949148332 scopus 로고    scopus 로고
    • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    • D.J. Hogan, D.P. Riordan, A.P. Gerber, D. Herschlang, and P.O. Brown Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system PLoS Biol. 6 10 2008 e255 10.1371/journal.pbio.0060255
    • (2008) PLoS Biol. , vol.6 , Issue.10 , pp. 255
    • Hogan, D.J.1    Riordan, D.P.2    Gerber, A.P.3    Herschlang, D.4    Brown, P.O.5
  • 26
    • 34249316905 scopus 로고    scopus 로고
    • RNA-binding proteins: Modular design for efficient function
    • B.M. Lunde, C. Moore, and G. Varani RNA-binding proteins: modular design for efficient function Nat. Rev. Mol. Cell Biol. 8 2007 479 490
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 479-490
    • Lunde, B.M.1    Moore, C.2    Varani, G.3
  • 27
    • 0028054162 scopus 로고
    • Selection of a subset of mRNAs from combinatorial 3′ untranslated region libraries using neuronal RNA-binding protein Hel-N1
    • F.B. Gao, C.C. Carson, T. Levine, and J.D. Keene Selection of a subset of mRNAs from combinatorial 3′ untranslated region libraries using neuronal RNA-binding protein Hel-N1 Proc. Natl. Acad. Sci. U.S.A. 91 1994 11207 11211
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 11207-11211
    • Gao, F.B.1    Carson, C.C.2    Levine, T.3    Keene, J.D.4
  • 28
    • 0034687794 scopus 로고    scopus 로고
    • Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
    • S.A. Tenenbaum, C.C. Carson, P.J. Lager, and J.D. Keene Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays Proc. Natl. Acad. Sci. U.S.A. 97 2000 14085 14090
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 14085-14090
    • Tenenbaum, S.A.1    Carson, C.C.2    Lager, P.J.3    Keene, J.D.4
  • 29
    • 10044282898 scopus 로고    scopus 로고
    • A systems view of mRNP biology
    • H. Hieronymus, and P.A. Silver A systems view of mRNP biology Genes Dev. 18 2004 2845 2860
    • (2004) Genes Dev. , vol.18 , pp. 2845-2860
    • Hieronymus, H.1    Silver, P.A.2
  • 30
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: Coordination of post-transcriptional events
    • J.D. Keene RNA regulons: coordination of post-transcriptional events Nat. Rev. Gen. 8 2007 533 543
    • (2007) Nat. Rev. Gen. , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 31
    • 34547233180 scopus 로고    scopus 로고
    • Systems perspectives on mRNA processing
    • A.E. McKee, and P.A. Silver Systems perspectives on mRNA processing Cell Res. 17 2007 581 590
    • (2007) Cell Res. , vol.17 , pp. 581-590
    • McKee, A.E.1    Silver, P.A.2
  • 32
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • A.P. Gerber, D. Herschlag, and P.O. Brown Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast PLoS Biol. 2 2004 E79
    • (2004) PLoS Biol. , vol.2 , pp. 79
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 33
    • 33645217973 scopus 로고    scopus 로고
    • Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
    • A.P. Gerber, S. Luschnig, M.A. Krasnow, P.O. Brown, and D. Herschlag Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster Proc. Natl. Acad. Sci. U.S.A. 103 2006 4487 4492
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 4487-4492
    • Gerber, A.P.1    Luschnig, S.2    Krasnow, M.A.3    Brown, P.O.4    Herschlag, D.5
  • 35
    • 33751213557 scopus 로고    scopus 로고
    • Pathways for mRNA localization in the cytoplasm
    • K. Czaplinski, and R.H. Singer Pathways for mRNA localization in the cytoplasm Trends Biochem. Sci. 31 2006 687 693
    • (2006) Trends Biochem. Sci. , vol.31 , pp. 687-693
    • Czaplinski, K.1    Singer, R.H.2
  • 36
    • 27944508215 scopus 로고    scopus 로고
    • CLIP: A method for identifying protein-RNA interaction sites in living cells
    • J. Ule, K. Jensen, A. Mele, and R.B. Darnell CLIP: a method for identifying protein-RNA interaction sites in living cells Methods Mol. Biol. 37 2005 376 386
    • (2005) Methods Mol. Biol. , vol.37 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 37
    • 33845275018 scopus 로고    scopus 로고
    • RIP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    • J.D. Keene, J.M. Komisarow, and M.B. Friedersdorf RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts Nat. Protoc. 1 2006 302 307
    • (2006) Nat. Protoc. , vol.1 , pp. 302-307
    • Keene, J.D.1    Komisarow, J.M.2    Friedersdorf, M.B.3
  • 39
    • 84868100738 scopus 로고    scopus 로고
    • Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions
    • M. Scheibe, F. Butter, M. Hafner, T. Tuschl, and M. Mann Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions Nucleic Acids Res. 40 2012 9897 9902
    • (2012) Nucleic Acids Res. , vol.40 , pp. 9897-9902
    • Scheibe, M.1    Butter, F.2    Hafner, M.3    Tuschl, T.4    Mann, M.5
  • 40
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • C. Zhang, and R.B. Darnell Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data Nat. Biotechnol. 29 2011 607 614
    • (2011) Nat. Biotechnol. , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2
  • 43
    • 78049275913 scopus 로고    scopus 로고
    • RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins
    • H. Kazan, D. Ray, E.T. Chan, T.R. Hughes, and Q. Morris RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins PLoS Comput. Biol. 6 7 2010 e1000832 10.1371/journal.pcbi.1000832
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.7 , pp. 1000832
    • Kazan, H.1    Ray, D.2    Chan, E.T.3    Hughes, T.R.4    Morris, Q.5
  • 44
    • 33750222859 scopus 로고    scopus 로고
    • Sequence-specific binding of single-stranded RNA: Is there a code for recognition?
    • S.D. Auweter, F.C. Oberstrass, and F.H. Allain Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res. 34 2006 4943 4959
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4943-4959
    • Auweter, S.D.1    Oberstrass, F.C.2    Allain, F.H.3
  • 45
    • 84255163357 scopus 로고    scopus 로고
    • Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1
    • X. Wang, L. Juan, J. Lv, K. Wang, J.R. Sanford, and Y. Liu Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1 BMC Genomics 12 Suppl. 5 2011 S8
    • (2011) BMC Genomics , vol.12 , Issue.SUPPL. 5 , pp. 8
    • Wang, X.1    Juan, L.2    Lv, J.3    Wang, K.4    Sanford, J.R.5    Liu, Y.6
  • 46
    • 58249111738 scopus 로고    scopus 로고
    • Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    • M.A. Jonikas, R.J. Radmer, A. Laederach, R. Das, S. Pearlman, D. Herschlag, and R.B. Altman Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters RNA 15 2009 189 199
    • (2009) RNA , vol.15 , pp. 189-199
    • Jonikas, M.A.1    Radmer, R.J.2    Laederach, A.3    Das, R.4    Pearlman, S.5    Herschlag, D.6    Altman, R.B.7
  • 47
    • 0035883742 scopus 로고    scopus 로고
    • Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. Elegans germ cell development
    • M.H. Lee, and T. Schedl Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development Genes Dev. 15 2001 2408 2420
    • (2001) Genes Dev. , vol.15 , pp. 2408-2420
    • Lee, M.H.1    Schedl, T.2
  • 48
  • 49
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 50
    • 35548973466 scopus 로고    scopus 로고
    • Functional specificity among ribosomal proteins regulates gene expression
    • S. Komili, N.G. Farny, F.P. Roth, and P.A. Silver Functional specificity among ribosomal proteins regulates gene expression Cell 131 2007 557 571
    • (2007) Cell , vol.131 , pp. 557-571
    • Komili, S.1    Farny, N.G.2    Roth, F.P.3    Silver, P.A.4
  • 51
    • 40449138572 scopus 로고    scopus 로고
    • Post-transcriptional gene regulation: From genome-wide studies to principles
    • R.E. Halbeisen, A. Galgano, T. Scherrer, and A.P. Gerber Post-transcriptional gene regulation: from genome-wide studies to principles Cell. Mol. Life Sci. 65 2008 798 813
    • (2008) Cell. Mol. Life Sci. , vol.65 , pp. 798-813
    • Halbeisen, R.E.1    Galgano, A.2    Scherrer, T.3    Gerber, A.P.4
  • 53
    • 0024439456 scopus 로고
    • The iron-responsive element binding protein: A method for the affinity purification of a regulatory RNA-binding protein
    • T.A. Rouault, M.W. Hentze, D.J. Haile, J.B. Harford, and R.D. Klausner The iron-responsive element binding protein: a method for the affinity purification of a regulatory RNA-binding protein Proc. Natl. Acad. Sci. U.S.A. 86 1989 5768 5772
    • (1989) Proc. Natl. Acad. Sci. U.S.A. , vol.86 , pp. 5768-5772
    • Rouault, T.A.1    Hentze, M.W.2    Haile, D.J.3    Harford, J.B.4    Klausner, R.D.5
  • 54
    • 84934434641 scopus 로고    scopus 로고
    • Isolation of a sequence-specific RNA binding protein, polypyrimidine tract binding protein, using RNA affinity chromatography
    • S. Sharma Isolation of a sequence-specific RNA binding protein, polypyrimidine tract binding protein, using RNA affinity chromatography Methods Mol. Biol. 488 2008 1 8
    • (2008) Methods Mol. Biol. , vol.488 , pp. 1-8
    • Sharma, S.1
  • 56
    • 0035864175 scopus 로고    scopus 로고
    • Sephadex-binding RNA ligands: Rapid affinity purification of RNA from complex RNA mixtures
    • C. Srisawat, I.J. Goldstein, and D.R. Engelke Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures Nucleic Acids Res. 29 2 2001 e4
    • (2001) Nucleic Acids Res. , vol.29 , Issue.2 , pp. 4
    • Srisawat, C.1    Goldstein, I.J.2    Engelke, D.R.3
  • 57
    • 0035001466 scopus 로고    scopus 로고
    • Streptavidin aptamers: Affinity tags for the study of RNAs and ribonucleoproteins
    • C. Srisawat, and D.R. Engelke Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins RNA 7 2001 632 641
    • (2001) RNA , vol.7 , pp. 632-641
    • Srisawat, C.1    Engelke, D.R.2
  • 58
    • 0038152834 scopus 로고    scopus 로고
    • Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation
    • A.A. Leonov, P.V. Sergiev, A.A. Bogdanov, R. Brimacombe, and O.A. Dontsova Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation J. Biol. Chem. 278 2003 25664 25670
    • (2003) J. Biol. Chem. , vol.278 , pp. 25664-25670
    • Leonov, A.A.1    Sergiev, P.V.2    Bogdanov, A.A.3    Brimacombe, R.4    Dontsova, O.A.5
  • 59
    • 0036713096 scopus 로고    scopus 로고
    • Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components
    • Y. Li, and S. Altman Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components Nucleic Acids Res. 30 2002 3706 3711
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3706-3711
    • Li, Y.1    Altman, S.2
  • 60
    • 0021111044 scopus 로고
    • Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site
    • J. Carey, V. Cameron, P.L. de Haseth, and O.C. Uhlenbeck Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site Biochemistry 22 11 1983 2601 2610
    • (1983) Biochemistry , vol.22 , Issue.11 , pp. 2601-2610
    • Carey, J.1    Cameron, V.2    De Haseth, P.L.3    Uhlenbeck, O.C.4
  • 61
    • 0025145063 scopus 로고
    • Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method
    • V.J. Bardwell, and M. Wickens Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method Nucleic Acids Res. 18 1990 6587 6594
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6587-6594
    • Bardwell, V.J.1    Wickens, M.2
  • 62
    • 0033636518 scopus 로고    scopus 로고
    • Functional association of U2 snRNP with the ATP-independent spliceosomal complex e
    • R. Das, Z. Zhou, and R. Reed Functional association of U2 snRNP with the ATP-independent spliceosomal complex E Mol. Cell 5 2000 779 787
    • (2000) Mol. Cell , vol.5 , pp. 779-787
    • Das, R.1    Zhou, Z.2    Reed, R.3
  • 63
    • 79955630425 scopus 로고    scopus 로고
    • Efficient detection of RNA-protein interactions using tethered RNAs
    • H. Lioka, D. Loiselle, T.A. Haystead, and I.G. Macara Efficient detection of RNA-protein interactions using tethered RNAs Nucleic Acids Res. 39 8 2011 e53 10.1093/nar/gkq1316
    • (2011) Nucleic Acids Res. , vol.39 , Issue.8 , pp. 53
    • Lioka, H.1    Loiselle, D.2    Haystead, T.A.3    Macara, I.G.4
  • 64
    • 0032647058 scopus 로고    scopus 로고
    • Purification and depletion of RNP particles by antisense affinity chromatography
    • B.J. Blencowe, and A.I. Lamond Purification and depletion of RNP particles by antisense affinity chromatography Methods Mol. Biol. 118 1999 275 287
    • (1999) Methods Mol. Biol. , vol.118 , pp. 275-287
    • Blencowe, B.J.1    Lamond, A.I.2
  • 65
    • 0029763191 scopus 로고    scopus 로고
    • Purification of telomerase from Euplotes aediculatus: Requirement of a primer 3′ overhang
    • J. Lingner, and T.R. Cech Purification of telomerase from Euplotes aediculatus: requirement of a primer 3′ overhang Proc. Natl. Acad. Sci. U.S.A. 93 1996 10712 10717
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 10712-10717
    • Lingner, J.1    Cech, T.R.2
  • 66
    • 77953640328 scopus 로고    scopus 로고
    • Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52
    • Y. Soeno, Y. Taya, T. Stasyk, L.A. Huber, T. Aoba, and A. Huttenhofer Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52 RNA 16 2010 1293 1300
    • (2010) RNA , vol.16 , pp. 1293-1300
    • Soeno, Y.1    Taya, Y.2    Stasyk, T.3    Huber, L.A.4    Aoba, T.5    Huttenhofer, A.6
  • 67
    • 0036217930 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA
    • S.P. Walton, G.N. Stephanopoulos, M.L. Yarmush, and C.M. Roth Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA Biophys. J. 82 2002 366 377
    • (2002) Biophys. J. , vol.82 , pp. 366-377
    • Walton, S.P.1    Stephanopoulos, G.N.2    Yarmush, M.L.3    Roth, C.M.4
  • 69
    • 34249053165 scopus 로고    scopus 로고
    • RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation
    • J.R. Hogg, and K. Collins RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation RNA 13 2007 868 880
    • (2007) RNA , vol.13 , pp. 868-880
    • Hogg, J.R.1    Collins, K.2
  • 70
    • 0021111035 scopus 로고
    • Kinetic and thermodynamic characterization of the R17 coat protein-ribonucleic acid interaction
    • J. Carey, and O.C. Uhlenbeck Kinetic and thermodynamic characterization of the R17 coat protein-ribonucleic acid interaction Biochemistry 22 1983 2610 2615
    • (1983) Biochemistry , vol.22 , pp. 2610-2615
    • Carey, J.1    Uhlenbeck, O.C.2
  • 71
    • 0035933720 scopus 로고    scopus 로고
    • Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7
    • F. Lim, T.P. Downey, and D.S. Peabody Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7 J. Biol. Chem. 276 2001 22507 22513
    • (2001) J. Biol. Chem. , vol.276 , pp. 22507-22513
    • Lim, F.1    Downey, T.P.2    Peabody, D.S.3
  • 72
    • 84892981981 scopus 로고    scopus 로고
    • An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins
    • K. Leppek, and G. Stoecklin An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins Nucleic Acids Res. 42 2014 e13
    • (2014) Nucleic Acids Res. , vol.42 , pp. 13
    • Leppek, K.1    Stoecklin, G.2
  • 73
    • 84877708543 scopus 로고    scopus 로고
    • Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs
    • K. Leppek, J. Schott, S. Reitter, F. Poetz, M.C. Hammond, and G. Stoecklin Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs Cell 153 2013 869 881
    • (2013) Cell , vol.153 , pp. 869-881
    • Leppek, K.1    Schott, J.2    Reitter, S.3    Poetz, F.4    Hammond, M.C.5    Stoecklin, G.6
  • 74
    • 79953321612 scopus 로고    scopus 로고
    • Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach
    • B.P. Tsai, X. Wang, L. Huang, and M.L. Waterman Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach Mol. Cell. Proteomics 10 M110 2011 007385
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.M110 , pp. 007385
    • Tsai, B.P.1    Wang, X.2    Huang, L.3    Waterman, M.L.4
  • 75
    • 33645703441 scopus 로고    scopus 로고
    • A tandem affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking
    • C. Tagwerker, K. Flick, M. Cui, C. Guerrero, Y. Dou, B. Auer, P. Baldi, L. Huang, and P. Kaiser A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking Mol. Cell. Proteomics 5 2006 737 748
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 737-748
    • Tagwerker, C.1    Flick, K.2    Cui, M.3    Guerrero, C.4    Dou, Y.5    Auer, B.6    Baldi, P.7    Huang, L.8    Kaiser, P.9
  • 76
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork Comparative assessment of large-scale data sets of protein-protein interactions Nature 417 2002 399 403
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 79
    • 0028890360 scopus 로고
    • A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein
    • J.C. Swaffield, K. Melcher, and S.A. Johnston A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein Nature 374 1995 88 91
    • (1995) Nature , vol.374 , pp. 88-91
    • Swaffield, J.C.1    Melcher, K.2    Johnston, S.A.3
  • 80
    • 79960064577 scopus 로고    scopus 로고
    • RaPID: An aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes
    • B. Slobodin, and J.E. Gerst RaPID: an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes Methods Mol. Biol. 714 2011 387 406
    • (2011) Methods Mol. Biol. , vol.714 , pp. 387-406
    • Slobodin, B.1    Gerst, J.E.2
  • 81
    • 78149342808 scopus 로고    scopus 로고
    • A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes
    • B. Slobodin, and J.E. Gerst A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes RNA 16 2010 2277 2290
    • (2010) RNA , vol.16 , pp. 2277-2290
    • Slobodin, B.1    Gerst, J.E.2
  • 86
    • 79952202326 scopus 로고    scopus 로고
    • PAIR technology: Exon-specific RNA-binding protein isolation in live cells
    • T.J. Bell, E. Eiriksdottir, U. Langel, and J. Eberwine PAIR technology: exon-specific RNA-binding protein isolation in live cells Methods Mol. Biol. 683 2011 473 486
    • (2011) Methods Mol. Biol. , vol.683 , pp. 473-486
    • Bell, T.J.1    Eiriksdottir, E.2    Langel, U.3    Eberwine, J.4
  • 87
    • 26444560167 scopus 로고    scopus 로고
    • Direct isolation of specific RNA-interacting proteins using a novel affinity medium
    • D.G. Liu, and L. Sun Direct isolation of specific RNA-interacting proteins using a novel affinity medium Nucleic Acids Res. 33 2005 e132
    • (2005) Nucleic Acids Res. , vol.33 , pp. 132
    • Liu, D.G.1    Sun, L.2
  • 88
    • 42949118288 scopus 로고    scopus 로고
    • Ribotrap: Targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs
    • D.L. Beach, and J.D. Keene Ribotrap: targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs Methods Mol. Biol. 419 2008 69 91
    • (2008) Methods Mol. Biol. , vol.419 , pp. 69-91
    • Beach, D.L.1    Keene, J.D.2
  • 89
    • 77955107974 scopus 로고    scopus 로고
    • RNase-assisted RNA chromatography
    • G. Michlewski, and J.F. Caceres RNase-assisted RNA chromatography RNA 16 2010 1673 1678
    • (2010) RNA , vol.16 , pp. 1673-1678
    • Michlewski, G.1    Caceres, J.F.2
  • 90
    • 84869990948 scopus 로고    scopus 로고
    • Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes
    • C. Gong, M.W. Popp, and L.E. Maquat Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes Methods 58 2012 88 93
    • (2012) Methods , vol.58 , pp. 88-93
    • Gong, C.1    Popp, M.W.2    Maquat, L.E.3
  • 92
    • 84869988685 scopus 로고    scopus 로고
    • MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs
    • J.H. Yoon, S. Srikantan, and M. Gorospe MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs Methods 58 2012 81 87
    • (2012) Methods , vol.58 , pp. 81-87
    • Yoon, J.H.1    Srikantan, S.2    Gorospe, M.3
  • 93
    • 84863741439 scopus 로고    scopus 로고
    • Chromatin isolation by RNA purification (ChIRP)
    • C. Chu, J. Quinn, and H.Y. Chang Chromatin isolation by RNA purification (ChIRP) J. Vis. Exp. 2012
    • (2012) J. Vis. Exp.
    • Chu, C.1    Quinn, J.2    Chang, H.Y.3
  • 94
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: Genomics, evolution, and mechanisms
    • I. Ulitsky, and D.P. Bartel LincRNAs: genomics, evolution, and mechanisms Cell 154 2013 26 46
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 95
    • 84907264117 scopus 로고    scopus 로고
    • Current protocols in molecular biology/edited by Frederick M Ausubel [et al.]. Chapter 21, Unit 21 25
    • Simon, M.D. (2013) Capture hybridization analysis of RNA targets (CHART), Current protocols in molecular biology/edited by Frederick M Ausubel [et al.]. Chapter 21, Unit 21 25.
    • (2013) Capture Hybridization Analysis of RNA Targets (CHART)
    • Simon, M.D.1
  • 98
    • 79955379829 scopus 로고    scopus 로고
    • RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5′ splice site
    • A. Kar, K. Fushimi, X. Zhou, P. Ray, C. Shi, X. Chen, Z. Liu, S. Chen, and J.Y. Wu RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5′ splice site Mol. Cell. Biol. 31 2011 1812 1821
    • (2011) Mol. Cell. Biol. , vol.31 , pp. 1812-1821
    • Kar, A.1    Fushimi, K.2    Zhou, X.3    Ray, P.4    Shi, C.5    Chen, X.6    Liu, Z.7    Chen, S.8    Wu, J.Y.9
  • 99
    • 31144443606 scopus 로고    scopus 로고
    • The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex
    • G.P. Patel, S. Ma, and J. Bag The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex Nucleic Acids Res. 33 2005 7074 7089
    • (2005) Nucleic Acids Res. , vol.33 , pp. 7074-7089
    • Patel, G.P.1    Ma, S.2    Bag, J.3
  • 100
    • 0031829287 scopus 로고    scopus 로고
    • A sequence-specific RNA-binding protein complements apobec-1 to edit apolipoprotein B mRNA
    • A. Mehta, and D.M. Driscoll A sequence-specific RNA-binding protein complements apobec-1 To edit apolipoprotein B mRNA Mol. Cell. Biol. 18 1998 4426 4432
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 4426-4432
    • Mehta, A.1    Driscoll, D.M.2
  • 101
    • 81255210913 scopus 로고    scopus 로고
    • Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3′ UTR structures
    • A.M. Ward, K. Bidet, A. Yinglin, S.G. Ler, K. Hogue, W. Blackstock, J. Gunaratne, and M.A. Garcia-Blanco Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3′ UTR structures RNA Biol. 8 2011 1173 1186
    • (2011) RNA Biol. , vol.8 , pp. 1173-1186
    • Ward, A.M.1    Bidet, K.2    Yinglin, A.3    Ler, S.G.4    Hogue, K.5    Blackstock, W.6    Gunaratne, J.7    Garcia-Blanco, M.A.8
  • 102
    • 81755176093 scopus 로고    scopus 로고
    • HnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene
    • I. Talukdar, S. Sen, R. Urbano, J. Thompson, J.R. Yates 3rd, and N.J. Webster HnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene PLoS ONE 6 2011 e27869
    • (2011) PLoS ONE , vol.6 , pp. 27869
    • Talukdar, I.1    Sen, S.2    Urbano, R.3    Thompson, J.4    Yates, J.R.5    Webster, N.J.6
  • 103
    • 33745592162 scopus 로고    scopus 로고
    • Identification of cellular factors associated with the 3′-nontranslated region of the hepatitis C virus genome
    • D. Harris, Z. Zhang, B. Chaubey, and V.N. Pandey Identification of cellular factors associated with the 3′-nontranslated region of the hepatitis C virus genome Mol. Cell. Proteomics 5 2006 1006 1018
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1006-1018
    • Harris, D.1    Zhang, Z.2    Chaubey, B.3    Pandey, V.N.4
  • 105
    • 84885051211 scopus 로고    scopus 로고
    • Mass spectrometry-based identification of proteins interacting with nucleic acids
    • A. Tacheny, M. Dieu, T. Arnould, and P. Renard Mass spectrometry-based identification of proteins interacting with nucleic acids J. Proteomics 94 2013 89 109
    • (2013) J. Proteomics , vol.94 , pp. 89-109
    • Tacheny, A.1    Dieu, M.2    Arnould, T.3    Renard, P.4
  • 106
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 17 1999 994 999
    • (1999) Nat. Biotechnol. , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 107
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • S.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics. 1 2002 376 386
    • (2002) Mol. Cell. Proteomics. , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 108
    • 79551474552 scopus 로고    scopus 로고
    • Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome
    • L. Ly, and V.C. Wasinger Protein and peptide fractionation, enrichment and depletion: tools for the complex proteome Proteomics 11 2011 513 534
    • (2011) Proteomics , vol.11 , pp. 513-534
    • Ly, L.1    Wasinger, V.C.2
  • 109
    • 11244297888 scopus 로고    scopus 로고
    • MudPIT: A powerful proteomics tool for discovery
    • E.C. Schirmer, J.R. Yates 3rd, and L. Gerace MudPIT: a powerful proteomics tool for discovery Discov. Med. 3 2003 38 39
    • (2003) Discov. Med. , vol.3 , pp. 38-39
    • Schirmer, E.C.1    Yates, J.R.2    Gerace, L.3
  • 110
    • 7044272280 scopus 로고    scopus 로고
    • Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
    • S. Mili, and J.A. Steitz Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses RNA 10 2004 1692 1694
    • (2004) RNA , vol.10 , pp. 1692-1694
    • Mili, S.1    Steitz, J.A.2
  • 111
    • 0018432123 scopus 로고
    • Ultraviolet light-induced crosslinking of mRNA to proteins
    • J.R. Greenberg Ultraviolet light-induced crosslinking of mRNA to proteins Nucleic Acids Res. 6 1979 715 732
    • (1979) Nucleic Acids Res. , vol.6 , pp. 715-732
    • Greenberg, J.R.1
  • 113
    • 0036354598 scopus 로고    scopus 로고
    • Analyzing mRNA-protein complexes using a yeast three-hybrid system
    • D.S. Bernstein, N. Buter, C. Stumpf, and M. Wickens Analyzing mRNA-protein complexes using a yeast three-hybrid system Methods 26 2002 123 141
    • (2002) Methods , vol.26 , pp. 123-141
    • Bernstein, D.S.1    Buter, N.2    Stumpf, C.3    Wickens, M.4
  • 114
    • 0029868515 scopus 로고    scopus 로고
    • Selection of RNA-binding peptides in vivo
    • K. Harada, S.S. Martin, and A.D. Frankel Selection of RNA-binding peptides in vivo Nature 380 1996 175 179
    • (1996) Nature , vol.380 , pp. 175-179
    • Harada, K.1    Martin, S.S.2    Frankel, A.D.3
  • 115
  • 117
    • 0025162336 scopus 로고
    • A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activation
    • S. Roy, U. Delling, C.H. Chen, C.A. Rosen, and N. Sonenberg A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activation Genes Dev. 4 1990 1365 1373
    • (1990) Genes Dev. , vol.4 , pp. 1365-1373
    • Roy, S.1    Delling, U.2    Chen, C.H.3    Rosen, C.A.4    Sonenberg, N.5
  • 118
    • 0025333764 scopus 로고
    • Activation of transcription by HIV-1 Tat protein tethered to nascent RNA through another protein
    • C. Southgate, M.L. Zapp, and M.R. Green Activation of transcription by HIV-1 Tat protein tethered to nascent RNA through another protein Nature 345 1990 640 642
    • (1990) Nature , vol.345 , pp. 640-642
    • Southgate, C.1    Zapp, M.L.2    Green, M.R.3
  • 119
    • 0032516079 scopus 로고    scopus 로고
    • A novel glutamine-RNA interaction identified by screening libraries in mammalian cells
    • R. Tan, and A.D. Frankel A novel glutamine-RNA interaction identified by screening libraries in mammalian cells Proc. Natl. Acad. Sci. U.S.A. 95 1998 4247 4252
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 4247-4252
    • Tan, R.1    Frankel, A.D.2
  • 120
    • 84868156900 scopus 로고    scopus 로고
    • A cell-based method for screening RNA-protein interactions: Identification of constitutive transport element-interacting proteins
    • R.L. Nakamura, S.G. Landt, E. Mai, J. Nejim, L. Chen, and A.D. Frankel A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins PLoS ONE 7 2012 e48194
    • (2012) PLoS ONE , vol.7 , pp. 48194
    • Nakamura, R.L.1    Landt, S.G.2    Mai, E.3    Nejim, J.4    Chen, L.5    Frankel, A.D.6
  • 121
    • 0027265641 scopus 로고
    • Cloning of a cDNA encoding an RNA binding protein by screening expression libraries using a northwestern strategy
    • Z. Qian, and J. Wilusz Cloning of a cDNA encoding an RNA binding protein by screening expression libraries using a northwestern strategy Anal. Biochem. 212 1993 547 554
    • (1993) Anal. Biochem. , vol.212 , pp. 547-554
    • Qian, Z.1    Wilusz, J.2
  • 122
    • 0017367397 scopus 로고
    • Screening lambdagt recombinant clones by hybridization to single plaques in situ
    • W.D. Benton, and R.W. Davis Screening lambdagt recombinant clones by hybridization to single plaques in situ Science 196 1977 180 182
    • (1977) Science , vol.196 , pp. 180-182
    • Benton, W.D.1    Davis, R.W.2
  • 123
    • 0343963539 scopus 로고    scopus 로고
    • Detection and isolation of RNA-binding proteins by RNA-ligand screening of a cDNA expression library
    • R. Sagesser, E. Martinez, M. Tsagris, and M. Tabler Detection and isolation of RNA-binding proteins by RNA-ligand screening of a cDNA expression library Nucleic Acids Res. 25 1997 3816 3822
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3816-3822
    • Sagesser, R.1    Martinez, E.2    Tsagris, M.3    Tabler, M.4
  • 124
    • 0042890326 scopus 로고    scopus 로고
    • A bromodomain-containing protein from tomato specifically binds potato spindle tuber viroid RNA in vitro and in vivo
    • A.E. Martinez de Alba, R. Sagesser, M. Tabler, and M. Tsagris A bromodomain-containing protein from tomato specifically binds potato spindle tuber viroid RNA in vitro and in vivo J. Virol. 77 2003 9685 9694
    • (2003) J. Virol. , vol.77 , pp. 9685-9694
    • Martinez De Alba, A.E.1    Sagesser, R.2    Tabler, M.3    Tsagris, M.4
  • 125
    • 0031854986 scopus 로고    scopus 로고
    • Man-made cell-like compartments for molecular evolution
    • D.S. Tawfik, and A.D. Griffiths Man-made cell-like compartments for molecular evolution Nat. Biotechnol. 16 1998 652 656
    • (1998) Nat. Biotechnol. , vol.16 , pp. 652-656
    • Tawfik, D.S.1    Griffiths, A.D.2
  • 126
    • 56049091246 scopus 로고    scopus 로고
    • Cell-free selection of RNA-binding proteins using in vitro compartmentalization
    • Y. Chen, J. Mandic, and G. Varani Cell-free selection of RNA-binding proteins using in vitro compartmentalization Nucleic Acids Res. 36 2008 e128
    • (2008) Nucleic Acids Res. , vol.36 , pp. 128
    • Chen, Y.1    Mandic, J.2    Varani, G.3
  • 127
    • 84868280186 scopus 로고    scopus 로고
    • Directed evolution of proteins through in vitro protein synthesis in liposomes
    • T. Nishikawa, T. Sunami, T. Matsuura, and T. Yomo Directed evolution of proteins through in vitro protein synthesis in liposomes J. Nucleic Acids 2012 2012 10.1155/2012/923214
    • (2012) J. Nucleic Acids , vol.2012
    • Nishikawa, T.1    Sunami, T.2    Matsuura, T.3    Yomo, T.4
  • 128
    • 84857165856 scopus 로고    scopus 로고
    • A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution
    • A. Fallah-Araghi, J.C. Baret, M. Ryckelynck, and A.D. Griffiths A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution Lab Chip 12 2012 882 891
    • (2012) Lab Chip , vol.12 , pp. 882-891
    • Fallah-Araghi, A.1    Baret, J.C.2    Ryckelynck, M.3    Griffiths, A.D.4
  • 129
    • 3042733142 scopus 로고    scopus 로고
    • A new method for the reconstitution of membrane proteins into giant unilamellar vesicles
    • P. Girard, J. Pecreaux, G. Lenoir, P. Falson, J.L. Rigaud, and P. Bassereau A new method for the reconstitution of membrane proteins into giant unilamellar vesicles Biophys. J. 87 2004 419 429
    • (2004) Biophys. J. , vol.87 , pp. 419-429
    • Girard, P.1    Pecreaux, J.2    Lenoir, G.3    Falson, P.4    Rigaud, J.L.5    Bassereau, P.6
  • 130
    • 0029615981 scopus 로고
    • Analysis of RNA-binding proteins by in vitro genetic selection: Identification of an amino acid residue important for locking U1A onto its RNA target
    • I.A. Laird-Offringa, and J.G. Belasco Analysis of RNA-binding proteins by in vitro genetic selection: Identification of an amino acid residue important for locking U1A onto its RNA target Proc. Natl. Acad. Sci. 92 1995 11859 11863
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 11859-11863
    • Laird-Offringa, I.A.1    Belasco, J.G.2
  • 131
    • 0030892127 scopus 로고    scopus 로고
    • Phage display of RNA binding zinc fingers from transcription factor IIIA
    • W.J. Friesen, and M.K. Darby Phage display of RNA binding zinc fingers from transcription factor IIIA J. Biol. Chem. 272 1997 10994 10997
    • (1997) J. Biol. Chem. , vol.272 , pp. 10994-10997
    • Friesen, W.J.1    Darby, M.K.2
  • 132
    • 0030817279 scopus 로고    scopus 로고
    • RNA-peptide fusions for the in vitro selection of peptides and proteins
    • R.W. Roberts, and J.W. Szostak RNA-peptide fusions for the in vitro selection of peptides and proteins Proc. Natl. Acad. Sci. U.S.A. 94 1997 12297 12302
    • (1997) Proc. Natl. Acad. Sci. U.S.A. , vol.94 , pp. 12297-12302
    • Roberts, R.W.1    Szostak, J.W.2
  • 133
    • 0031559943 scopus 로고    scopus 로고
    • In vitro virus: Bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro
    • N. Nemoto, E. Miyamoto-Sato, Y. Husimi, and H. Yanagawa In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro FEBS Lett. 414 1997 405 408
    • (1997) FEBS Lett. , vol.414 , pp. 405-408
    • Nemoto, N.1    Miyamoto-Sato, E.2    Husimi, Y.3    Yanagawa, H.4
  • 135
    • 0037011406 scopus 로고    scopus 로고
    • Screening and selection methods for large-scale analysis of protein function
    • H. Lin, and V.W. Cornish Screening and selection methods for large-scale analysis of protein function Angew. Chem. 41 2002 4402 4425
    • (2002) Angew. Chem. , vol.41 , pp. 4402-4425
    • Lin, H.1    Cornish, V.W.2
  • 136
    • 78649736872 scopus 로고    scopus 로고
    • A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes
    • T. Scherrer, N. Mittal, S.C. Janga, and A.P. Gerber A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes PLoS ONE 5 2010 e15499
    • (2010) PLoS ONE , vol.5 , pp. 15499
    • Scherrer, T.1    Mittal, N.2    Janga, S.C.3    Gerber, A.P.4
  • 137
    • 77958594113 scopus 로고    scopus 로고
    • Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae
    • N.G. Tsvetanova, D.M. Klass, J. Salzman, and P.O. Brown Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae PloS ONE 5 2010
    • (2010) PloS ONE , vol.5
    • Tsvetanova, N.G.1    Klass, D.M.2    Salzman, J.3    Brown, P.O.4
  • 139
    • 12944327374 scopus 로고    scopus 로고
    • Mammalian Staufen1 recruits Upf1 to specific mRNA 3′ UTRs so as to elicit mRNA decay
    • Y.K. Kim, L. Furic, L. Desgroseillers, and L.E. Maquat Mammalian Staufen1 recruits Upf1 to specific mRNA 3′ UTRs so as to elicit mRNA decay Cell 120 2005 195 208
    • (2005) Cell , vol.120 , pp. 195-208
    • Kim, Y.K.1    Furic, L.2    Desgroseillers, L.3    Maquat, L.E.4
  • 140
    • 38349140689 scopus 로고    scopus 로고
    • The regulatory element in the 3′-untranslated region of human papillomavirus 16 inhibits expression by binding CUG-binding protein 1
    • R. Goraczniak, and S.I. Gunderson The regulatory element in the 3′-untranslated region of human papillomavirus 16 inhibits expression by binding CUG-binding protein 1 J. Biol. Chem. 283 2008 2286 2296
    • (2008) J. Biol. Chem. , vol.283 , pp. 2286-2296
    • Goraczniak, R.1    Gunderson, S.I.2
  • 141
    • 67149111643 scopus 로고    scopus 로고
    • Prediction and integration of regulatory and protein-protein interactions
    • D. Wichadakul, J. McDermott, and R. Samudrala Prediction and integration of regulatory and protein-protein interactions Methods Mol. Biol. 541 2009 101 143
    • (2009) Methods Mol. Biol. , vol.541 , pp. 101-143
    • Wichadakul, D.1    McDermott, J.2    Samudrala, R.3
  • 142
  • 143
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • C. Laing, and T. Schlick Computational approaches to 3D modeling of RNA J. Phys. Condens. Matter 22 2010 283101
    • (2010) J. Phys. Condens. Matter , vol.22 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 144
    • 80255140476 scopus 로고    scopus 로고
    • RNA and protein 3D structure modeling: Similarities and differences
    • K. Rother, M. Rother, M. Boniecki, T. Puton, and J.M. Bujnicki RNA and protein 3D structure modeling: similarities and differences J. Mol. Model. 17 2011 2325 2336
    • (2011) J. Mol. Model. , vol.17 , pp. 2325-2336
    • Rother, K.1    Rother, M.2    Boniecki, M.3    Puton, T.4    Bujnicki, J.M.5
  • 145
    • 0033648805 scopus 로고    scopus 로고
    • Use of dimethyl sulfate to probe RNA structure in vivo
    • S.E. Wells, J.M. Hughes, A.H. Igel, and M. Ares Jr. Use of dimethyl sulfate to probe RNA structure in vivo Methods Enzymol. 318 2000 479 493
    • (2000) Methods Enzymol. , vol.318 , pp. 479-493
    • Wells, S.E.1    Hughes, J.M.2    Igel, A.H.3    Ares, M.4
  • 146
    • 0032319210 scopus 로고    scopus 로고
    • Following the folding of RNA with time-resolved synchrotron X-ray footprinting
    • B. Sclavi, S. Woodson, M. Sullivan, M. Chance, and M. Brenowitz Following the folding of RNA with time-resolved synchrotron X-ray footprinting Methods Enzymol. 295 1998 379 402
    • (1998) Methods Enzymol. , vol.295 , pp. 379-402
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.4    Brenowitz, M.5
  • 147
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
    • E.J. Merino, K.A. Wilkinson, J.L. Coughlan, and K.M. Weeks RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127 2005 4223 4231
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 148
    • 70349145411 scopus 로고    scopus 로고
    • Time-resolved RNA SHAPE chemistry: Quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution
    • S.A. Mortimer, and K.M. Weeks Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution Nat. Protoc. 4 2009 1413 1421
    • (2009) Nat. Protoc. , vol.4 , pp. 1413-1421
    • Mortimer, S.A.1    Weeks, K.M.2
  • 149
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • M. Zuker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Res. 9 1981 133 148
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 150
    • 33646867882 scopus 로고    scopus 로고
    • Memory efficient folding algorithms for circular RNA secondary structures
    • I.L. Hofacker, and P.F. Stadler Memory efficient folding algorithms for circular RNA secondary structures Bioinformatics 22 2006 1172 1176
    • (2006) Bioinformatics , vol.22 , pp. 1172-1176
    • Hofacker, I.L.1    Stadler, P.F.2
  • 151
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • C.B. Do, D.A. Woods, and S. Batzoglou CONTRAfold: RNA secondary structure prediction without physics-based models Bioinformatics 22 2006 e90 e98
    • (2006) Bioinformatics , vol.22 , pp. 90-e98
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 154
  • 155
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary structures
    • R. Das, and D. Baker Automated de novo prediction of native-like RNA tertiary structures Proc. Natl. Acad. Sci. U.S.A. 104 2007 14664 14669
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 14664-14669
    • Das, R.1    Baker, D.2
  • 156
    • 50549096615 scopus 로고    scopus 로고
    • IFoldRNA: Three-dimensional RNA structure prediction and folding
    • S. Sharma, F. Ding, and N.V. Dokholyan IFoldRNA: three-dimensional RNA structure prediction and folding Bioinformatics 24 2008 1951 1952
    • (2008) Bioinformatics , vol.24 , pp. 1951-1952
    • Sharma, S.1    Ding, F.2    Dokholyan, N.V.3
  • 157
    • 43749124906 scopus 로고    scopus 로고
    • RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA
    • H.M. Martinez, J.V. Maizel Jr., and B.A. Shapiro RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA J. Biomol. Struct. Dyn. 25 2008 669 683
    • (2008) J. Biomol. Struct. Dyn. , vol.25 , pp. 669-683
    • Martinez, H.M.1    Maizel, J.V.2    Shapiro, B.A.3
  • 159
    • 77949343955 scopus 로고    scopus 로고
    • Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins
    • L. Perez-Cano, and J. Fernandez-Recio Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins Proteins 78 2010 25 35
    • (2010) Proteins , vol.78 , pp. 25-35
    • Perez-Cano, L.1    Fernandez-Recio, J.2
  • 160
    • 79955638463 scopus 로고    scopus 로고
    • Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
    • H. Zhao, Y. Yang, and Y. Zhou Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets Nucleic Acids Res. 39 2011 3017 3025
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3017-3025
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 161
    • 33845865515 scopus 로고    scopus 로고
    • Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction
    • O.T. Kim, K. Yura, and N. Go Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction Nucleic Acids Res. 34 2006 6450 6460
    • (2006) Nucleic Acids Res. , vol.34 , pp. 6450-6460
    • Kim, O.T.1    Yura, K.2    Go, N.3
  • 162
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • C. Dominguez, R. Boelens, and A.M. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 164
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • D.W. Ritchie, and G.J. Kemp Protein docking using spherical polar Fourier correlations Proteins 39 2000 178 194
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 166
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • H.A. Gabb, R.M. Jackson, and M.J. Sternberg Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 272 1997 106 120
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 167
    • 84878654457 scopus 로고    scopus 로고
    • A novel protocol for three-dimensional structure prediction of RNA-protein complexes
    • Y. Huang, S. Liu, D. Guo, L. Li, and Y. Xiao A novel protocol for three-dimensional structure prediction of RNA-protein complexes Sci. Rep. 3 2013 1887
    • (2013) Sci. Rep. , vol.3 , pp. 1887
    • Huang, Y.1    Liu, S.2    Guo, D.3    Li, L.4    Xiao, Y.5
  • 168
  • 169
  • 170
    • 84907259326 scopus 로고    scopus 로고
    • High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs
    • P.N. Grozdanov, and C.C. Macdonald High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs Methods Mol. Biol. 1125 2014 187 208
    • (2014) Methods Mol. Biol. , vol.1125 , pp. 187-208
    • Grozdanov, P.N.1    Macdonald, C.C.2
  • 171
    • 0242497663 scopus 로고    scopus 로고
    • CLIP identifies Nova-regulated RNA networks in the brain
    • J. Ule, K.B. Jensen, M. Ruggiu, A. Mele, A. Ule, and R.B. Darnell CLIP identifies Nova-regulated RNA networks in the brain Science 302 2003 1212 1215
    • (2003) Science , vol.302 , pp. 1212-1215
    • Ule, J.1    Jensen, K.B.2    Ruggiu, M.3    Mele, A.4    Ule, A.5    Darnell, R.B.6
  • 172
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 173
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • S.E. Ong, and M. Mann Mass spectrometry-based proteomics turns quantitative Nat. Chem. Biol. 1 2005 252 262
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 177
    • 34047223024 scopus 로고    scopus 로고
    • Posttranscriptional expression regulation: What determines translation rates?
    • R. Brockmann, A. Beyer, J.J. Heinisch, and T. Wilhelm Posttranscriptional expression regulation: what determines translation rates? PLoS Comput. Biol. 3 2007 e57
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 57
    • Brockmann, R.1    Beyer, A.2    Heinisch, J.J.3    Wilhelm, T.4
  • 181
    • 34250313519 scopus 로고    scopus 로고
    • Local activation of yeast ASH1 mRNA translation through phosphorylation of Khd1p by the casein kinase Yck1p
    • N. Paquin, M. Menade, G. Poirier, D. Donato, E. Drouet, and P. Chartrand Local activation of yeast ASH1 mRNA translation through phosphorylation of Khd1p by the casein kinase Yck1p Mol. Cell 26 2007 795 809
    • (2007) Mol. Cell , vol.26 , pp. 795-809
    • Paquin, N.1    Menade, M.2    Poirier, G.3    Donato, D.4    Drouet, E.5    Chartrand, P.6
  • 182
    • 0037213715 scopus 로고    scopus 로고
    • Gene expression and the myth of the average cell
    • J.M. Levsky, and R.H. Singer Gene expression and the myth of the average cell Trends Cell Biol. 13 2003 4 6
    • (2003) Trends Cell Biol. , vol.13 , pp. 4-6
    • Levsky, J.M.1    Singer, R.H.2
  • 183
    • 0141561891 scopus 로고    scopus 로고
    • Integrating 'omic' information: A bridge between genomics and systems biology
    • H. Ge, A.J. Walhout, and M. Vidal Integrating 'omic' information: a bridge between genomics and systems biology Trends Genetics 19 2003 551 560
    • (2003) Trends Genetics , vol.19 , pp. 551-560
    • Ge, H.1    Walhout, A.J.2    Vidal, M.3


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