메뉴 건너뛰기




Volumn 419, Issue , 2008, Pages 69-91

Ribotrap: Targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs

(2)  Beach, Dale L a   Keene, Jack D a  

a NONE

Author keywords

Aptamer; MS2; Post transcriptional regulation; Ribonomics; RNA binding protein; RNP

Indexed keywords

FUNGAL RNA; RIBONUCLEOPROTEIN; RNA; RNA BINDING PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 42949118288     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-033-1_5     Document Type: Article
Times cited : (28)

References (51)
  • 1
    • 23444446940 scopus 로고    scopus 로고
    • Post-transcriptional operons and regulons co-ordinating gene expression
    • Keene, J. D., and Lager, P. J. (2005) Post-transcriptional operons and regulons co-ordinating gene expression. Chromosome Res 13, 327-37.
    • (2005) Chromosome Res , vol.13 , pp. 327-337
    • Keene, J.D.1    Lager, P.J.2
  • 2
    • 24644502657 scopus 로고    scopus 로고
    • From birth to death: The complex lives of eukaryotic mRNAs
    • Moore, M. J. (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514-8.
    • (2005) Science , vol.309 , pp. 1514-1518
    • Moore, M.J.1
  • 3
    • 0036351379 scopus 로고    scopus 로고
    • Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays
    • Tenenbaum, S. A., Lager, P. J., Carson, C. C, and Keene, J. D. (2002) Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26, 191-8.
    • (2002) Methods , vol.26 , pp. 191-198
    • Tenenbaum, S.A.1    Lager, P.J.2    Carson, C.C.3    Keene, J.D.4
  • 4
    • 0035912793 scopus 로고    scopus 로고
    • Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome
    • Keene, J. D. (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98, 7018-24.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 7018-7024
    • Keene, J.D.1
  • 5
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • Keene, J. D., and Tenenbaum, S. A. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9, 1161-7.
    • (2002) Mol Cell , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 6
    • 0034687794 scopus 로고    scopus 로고
    • Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
    • Tenenbaum, S. A., Carson, C. C, Lager, P. J., and Keene, J. D. (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci USA 97, 14085-90.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 14085-14090
    • Tenenbaum, S.A.1    Carson, C.C.2    Lager, P.J.3    Keene, J.D.4
  • 7
    • 33845275018 scopus 로고    scopus 로고
    • RIP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    • Keene, J. D., Komisarow, J. M., and Friedersdorf, M. B. (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protocols 1, 302-7.
    • (2006) Nat Protocols , vol.1 , pp. 302-307
    • Keene, J.D.1    Komisarow, J.M.2    Friedersdorf, M.B.3
  • 8
    • 0027367040 scopus 로고
    • Transport and localization of exogenous myelin basic protein mRNA microinjected into oligodendrocytes
    • Ainger, K, Avossa, D., Morgan, F., Hill, S. J., Barry, C, Barbarese, E., and Carson, J. H. (1993) Transport and localization of exogenous myelin basic protein mRNA microinjected into oligodendrocytes. J Cell Biol 123, 431-41.
    • (1993) J Cell Biol , vol.123 , pp. 431-441
    • Ainger, K.1    Avossa, D.2    Morgan, F.3    Hill, S.J.4    Barry, C.5    Barbarese, E.6    Carson, J.H.7
  • 9
    • 0024439456 scopus 로고
    • The iron-responsive element binding protein: A method for the affinity purification of a regulatory RNA-binding protein
    • Rouault, T. A., Hentze, M. W., Haile, D. J., Harford, J. B., and Klausner, R. D. (1989) The iron-responsive element binding protein: a method for the affinity purification of a regulatory RNA-binding protein. Proc Natl Acad Sci USA 86, 5768-72.
    • (1989) Proc Natl Acad Sci USA , 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
  • 10
    • 1642441710 scopus 로고    scopus 로고
    • Two-step affinity purification of the hepatitis C virus ribonucleoprotein complex
    • Waris, G., Sarker, S., and Siddiqui, A. (2004) Two-step affinity purification of the hepatitis C virus ribonucleoprotein complex. RNA 10, 321-9.
    • (2004) RNA , vol.10 , pp. 321-329
    • Waris, G.1    Sarker, S.2    Siddiqui, A.3
  • 12
    • 0032758073 scopus 로고    scopus 로고
    • StreptoTag: A novel method for the isolation of RNA-binding proteins
    • Bachler, M., Schroeder, R., and von Ahsen, U. (1999) StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA 5, 1509-16.
    • (1999) RNA , vol.5 , pp. 1509-1516
    • Bachler, M.1    Schroeder, R.2    Von Ahsen, U.3
  • 14
    • 0035864175 scopus 로고    scopus 로고
    • Sephadex-binding RNA ligands: Rapid affinity purification of RNA from complex RNA mixtures
    • Srisawat, C., Goldstein, I. J., and Engelke, D. R. (2001) Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res 29, E4.
    • (2001) Nucleic Acids Res , vol.29
    • Srisawat, C.1    Goldstein, I.J.2    Engelke, D.R.3
  • 15
    • 0035001466 scopus 로고    scopus 로고
    • Streptavidin aptamers: Affinity tags for the study of RNAs and ribonucleoproteins
    • Srisawat, C., and Engelke, D. R. (2001) Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 7, 632-41.
    • (2001) RNA , vol.7 , pp. 632-641
    • Srisawat, C.1    Engelke, D.R.2
  • 16
    • 0026630127 scopus 로고
    • In vitro selection of an RNA epitope immunologically cross-reactive with a peptide
    • Tsai, D. E., Kenan, D. J., and Keene, J. D. (1992) In vitro selection of an RNA epitope immunologically cross-reactive with a peptide. Proc Natl Acad Sci USA 89, 8864-8.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 8864-8868
    • Tsai, D.E.1    Kenan, D.J.2    Keene, J.D.3
  • 17
    • 0034644626 scopus 로고    scopus 로고
    • Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier
    • Takizawa, P. A., DeRisi, J. L., Wilhelm, J. E., and Vale, R. D. (2000) Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science 290, 341-4.
    • (2000) Science , vol.290 , pp. 341-344
    • Takizawa, P.A.1    DeRisi, J.L.2    Wilhelm, J.E.3    Vale, R.D.4
  • 18
    • 0034544815 scopus 로고    scopus 로고
    • Pre-mRNA processing factors are required for nuclear export
    • Brodsky, A. S., and Silver, P. A. (2000) Pre-mRNA processing factors are required for nuclear export. RNA 6, 1737-49.
    • (2000) RNA , vol.6 , pp. 1737-1749
    • Brodsky, A.S.1    Silver, P.A.2
  • 19
    • 0036242097 scopus 로고    scopus 로고
    • Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis
    • Jurica, M. S., Licklider, L. J., Gygi, S. R., Grigorieff, N., and Moore, M. J. (2002) Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8, 426-39.
    • (2002) RNA , vol.8 , pp. 426-439
    • Jurica, M.S.1    Licklider, L.J.2    Gygi, S.R.3    Grigorieff, N.4    Moore, M.J.5
  • 20
    • 32044436719 scopus 로고    scopus 로고
    • Sex-lethal imparts a sex-specific function to UNR by recruiting it to the msl-2 mRNA 3' UTR: Translational repression for dosage compensation
    • Duncan, K., Grskovic, M., Strein, C., Beckmann, K., Niggeweg, R., Abaza, I., Gebauer, F., Wilm, M., and Hentze, M. W. (2006) Sex-lethal imparts a sex-specific function to UNR by recruiting it to the msl-2 mRNA 3' UTR: translational repression for dosage compensation. Genes Dev 20, 368-79.
    • (2006) Genes Dev , vol.20 , pp. 368-379
    • Duncan, K.1    Grskovic, M.2    Strein, C.3    Beckmann, K.4    Niggeweg, R.5    Abaza, I.6    Gebauer, F.7    Wilm, M.8    Hentze, M.W.9
  • 21
    • 33745860086 scopus 로고    scopus 로고
    • Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions
    • Deckert, J., Hartmuth, K., Boehringer, D., Behzadnia, N., Will, C. L., Kastner, B., Stark, H., Urlaub, H., and Luhrmann, R. (2006) Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol Cell Biol 26, 5528-43.
    • (2006) Mol Cell Biol , vol.26 , pp. 5528-5543
    • Deckert, J.1    Hartmuth, K.2    Boehringer, D.3    Behzadnia, N.4    Will, C.L.5    Kastner, B.6    Stark, H.7    Urlaub, H.8    Luhrmann, R.9
  • 22
    • 16244398690 scopus 로고    scopus 로고
    • Identification of 40LoVe, a Xenopus hnRNP D family protein involved in localizing a TGF-beta-related mRNA during oogenesis
    • Czaplinski, K., Kocher, T., Schelder, M., Segref, A., Wilm, M., and Mattaj, I. W. (2005) Identification of 40LoVe, a Xenopus hnRNP D family protein involved in localizing a TGF-beta-related mRNA during oogenesis. Dev Cell 8, 505-15.
    • (2005) Dev Cell , vol.8 , pp. 505-515
    • Czaplinski, K.1    Kocher, T.2    Schelder, M.3    Segref, A.4    Wilm, M.5    Mattaj, I.W.6
  • 24
    • 12844273362 scopus 로고    scopus 로고
    • RNA-protein interactions in the yeast three-hybrid system: Affinity, sensitivity, and enhanced library screening
    • Hook, B., Bernstein, D., Zhang, B., and Wickens, M. (2005) RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening. RNA 11, 227-33.
    • (2005) RNA , vol.11 , pp. 227-233
    • Hook, B.1    Bernstein, D.2    Zhang, B.3    Wickens, M.4
  • 25
    • 8544254751 scopus 로고    scopus 로고
    • ASH1 mRNA anchoring requires reorganization of the Myo4p-She3p-She2p transport complex
    • Gonsalvez, G. B., Little, J. L., and Long, R. M. (2004) ASH1 mRNA anchoring requires reorganization of the Myo4p-She3p-She2p transport complex. J Biol Chem 279, 46286-94.
    • (2004) J Biol Chem , vol.279 , pp. 46286-46294
    • Gonsalvez, G.B.1    Little, J.L.2    Long, R.M.3
  • 26
    • 0033519623 scopus 로고    scopus 로고
    • Localization and anchoring of mRNA in budding yeast
    • Beach, D. L., Salmon, E. D., and Bloom, K. (1999) Localization and anchoring of mRNA in budding yeast. Curr Biol 9, 569-78.
    • (1999) Curr Biol , vol.9 , pp. 569-578
    • Beach, D.L.1    Salmon, E.D.2    Bloom, K.3
  • 29
    • 0028060580 scopus 로고
    • Mutations that increase the affinity of a translational repressor for RNA
    • Lim, F., and Peabody, D. S. (1994) Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res 22, 3748-52.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3748-3752
    • Lim, F.1    Peabody, D.S.2
  • 31
    • 0028070676 scopus 로고
    • Proteins binding to 5' untranslated region sites: A general mechanism for translational regulation of mRNAs in human and yeast cells
    • Stripecke, R., Oliveira, C. C., McCarthy, J. E., and Hentze, M. W. (1994) Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells. Mol Cell Biol 14, 5898-909.
    • (1994) Mol Cell Biol , vol.14 , pp. 5898-5909
    • Stripecke, R.1    Oliveira, C.C.2    McCarthy, J.E.3    Hentze, M.W.4
  • 32
    • 0035158326 scopus 로고    scopus 로고
    • ASH1 mRNA localization in three acts
    • Beach, D. L., and Bloom, K. (2001) ASH1 mRNA localization in three acts. Mol Biol Cell 12, 2567-77.
    • (2001) Mol Biol Cell , vol.12 , pp. 2567-2577
    • Beach, D.L.1    Bloom, K.2
  • 33
    • 0030875775 scopus 로고    scopus 로고
    • Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA
    • Long, R. M., Singer, R. H., Meng, X., Gonzalez, I., Nasmyth, K., and Jansen, R. P. (1997) Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA. Science 277, 383-7.
    • (1997) Science , vol.277 , pp. 383-387
    • Long, R.M.1    Singer, R.H.2    Meng, X.3    Gonzalez, I.4    Nasmyth, K.5    Jansen, R.P.6
  • 36
    • 0030930836 scopus 로고    scopus 로고
    • Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast
    • Takizawa, P. A., Sil, A., Swedlow, J. R., Herskowitz, I., and Vale, R. D. (1997) Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast. Nature 389, 90-3.
    • (1997) Nature , vol.389 , pp. 90-93
    • Takizawa, P.A.1    Sil, A.2    Swedlow, J.R.3    Herskowitz, I.4    Vale, R.D.5
  • 37
    • 2942692177 scopus 로고    scopus 로고
    • A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization
    • Gu, W., Deng, Y., Zenklusen, D., and Singer, R. H. (2004) A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization. Genes Dev 18, 1452-65.
    • (2004) Genes Dev , vol.18 , pp. 1452-1465
    • Gu, W.1    Deng, Y.2    Zenklusen, D.3    Singer, R.H.4
  • 39
    • 0033667456 scopus 로고    scopus 로고
    • A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling
    • Lopez, M. F., Berggren, K., Chernokalskaya, E., Lazarev, A., Robinson, M., and Patton, W. F. (2000) A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 21, 3673-83.
    • (2000) Electrophoresis , vol.21 , pp. 3673-3683
    • Lopez, M.F.1    Berggren, K.2    Chernokalskaya, E.3    Lazarev, A.4    Robinson, M.5    Patton, W.F.6
  • 40
    • 3142726606 scopus 로고    scopus 로고
    • Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning
    • Ambros, V., and Lee, R. C. (2004) Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning. Methods Mol Biol 265, 131-58.
    • (2004) Methods Mol Biol , vol.265 , pp. 131-158
    • Ambros, V.1    Lee, R.C.2
  • 41
    • 0035955361 scopus 로고    scopus 로고
    • An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    • Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-62.
    • (2001) Science , vol.294 , pp. 858-862
    • Lau, N.C.1    Lim, L.P.2    Weinstein, E.G.3    Bartel, D.P.4
  • 42
    • 13944262052 scopus 로고    scopus 로고
    • A custom microarray platform for analysis of microRNA gene expression
    • Thomson, J. M., Parker, J., Perou, C. M., and Hammond, S. M. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1, 47-53.
    • (2004) Nat Methods , vol.1 , pp. 47-53
    • Thomson, J.M.1    Parker, J.2    Perou, C.M.3    Hammond, S.M.4
  • 43
    • 27144543663 scopus 로고    scopus 로고
    • Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs
    • Raymond, C. K., Roberts, B. S., Garrett-Engele, P., Lim, L. P., and Johnson, J. M. (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 11, 1737-44.
    • (2005) RNA , vol.11 , pp. 1737-1744
    • Raymond, C.K.1    Roberts, B.S.2    Garrett-Engele, P.3    Lim, L.P.4    Johnson, J.M.5
  • 44
    • 0034571236 scopus 로고    scopus 로고
    • Proteins S7, S10, S16 and S19 of the human 40S ribosomal subunit are most resistant to dissociation by salt
    • Malygin, A. A., Shaulo, D. D., and Karpova, G. G. (2000) Proteins S7, S10, S16 and S19 of the human 40S ribosomal subunit are most resistant to dissociation by salt. Biochim Biophys Acta 1494, 213-6.
    • (2000) Biochim Biophys Acta , vol.1494 , pp. 213-216
    • Malygin, A.A.1    Shaulo, D.D.2    Karpova, G.G.3
  • 45
    • 0036436733 scopus 로고    scopus 로고
    • Capturing splicing complexes to study structure and mechanism
    • Jurica, M. S., and Moore, M. J. (2002) Capturing splicing complexes to study structure and mechanism. Methods 28, 336-45.
    • (2002) Methods , vol.28 , pp. 336-345
    • Jurica, M.S.1    Moore, M.J.2
  • 46
    • 2342487399 scopus 로고    scopus 로고
    • The composition of Staufen-containing RNA granules from human cells indicates their role in the regulated transport and translation of messenger RNAs
    • Villace, P., Marion, R. M., and Ortin, J. (2004) The composition of Staufen-containing RNA granules from human cells indicates their role in the regulated transport and translation of messenger RNAs. Nucleic Acids Res 32, 2411-20.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2411-2420
    • Villace, P.1    Marion, R.M.2    Ortin, J.3
  • 47
    • 0034757770 scopus 로고    scopus 로고
    • Proteomics: The move to mixtures
    • Peng, J., and Gygi, S. P. (2001) Proteomics: the move to mixtures. J Mass Spectrom 36, 1083-91.
    • (2001) J Mass Spectrom , vol.36 , pp. 1083-1091
    • Peng, J.1    Gygi, S.P.2
  • 48
    • 0029927505 scopus 로고    scopus 로고
    • Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels
    • Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68, 850-8.
    • (1996) Anal Chem , vol.68 , pp. 850-858
    • Shevchenko, A.1    Wilm, M.2    Vorm, O.3    Mann, M.4
  • 49
    • 8844253195 scopus 로고    scopus 로고
    • RNA integrity as a quality indicator during the first steps of RNP purifications: A comparison of yeast lysis methods
    • Lopez de Heredia, M., and Jansen, R. P. (2004) RNA integrity as a quality indicator during the first steps of RNP purifications: a comparison of yeast lysis methods. BMC Biochem 5, 14.
    • (2004) BMC Biochem , vol.5 , pp. 14
    • Lopez De Heredia, M.1    Jansen, R.P.2
  • 50
    • 0026577063 scopus 로고
    • Control of translational repression by protein-protein interactions
    • Peabody, D. S., and Ely, K. R. (1992) Control of translational repression by protein-protein interactions. Nucleic Acids Res 20, 1649-55.
    • (1992) Nucleic Acids Res , vol.20 , pp. 1649-1655
    • Peabody, D.S.1    Ely, K.R.2
  • 51
    • 0028586017 scopus 로고
    • Regulatable promoters of saccha-romyces cerevisiae: Comparison of transcriptional activity and their use for heterologous expression
    • Mumberg, D., Muller, R., and Funk, M. (1994) Regulatable promoters of saccha-romyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression. Nucleic Acids Res 22, 5767-68.
    • (1994) Nucleic Acids Res , vol.22 , pp. 5767-5768
    • Mumberg, D.1    Muller, R.2    Funk, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.