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Volumn 714, Issue , 2011, Pages 369-385

RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs

Author keywords

Immunopurification; Microarray; Post transcriptional gene regulation; RIP Chip; RNA binding protein

Indexed keywords

ANTIBODY; CELL EXTRACT; COMPLEMENTARY RNA; EDETIC ACID; FLUORESCENT DYE; G SUBSTRATE; G-SUBSTRATE; MICROSPHERE; NERVE PROTEIN; PUM1 PROTEIN, HUMAN; PUM2 PROTEIN, HUMAN; RIBONUCLEOPROTEIN; RNA; RNA BINDING PROTEIN; SEPHAROSE; STAPHYLOCOCCUS PROTEIN A;

EID: 79960062813     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-005-8_23     Document Type: Chapter
Times cited : (12)

References (57)
  • 1
    • 0037041395 scopus 로고    scopus 로고
    • An extensive network of coupling among gene expression machines
    • Maniatis, T., and Reed, R. (2002) An extensive network of coupling among gene expression machines, Nature 416, 499–506.
    • (2002) Nature , vol.416 , pp. 499-506
    • Maniatis, T.1    Reed, R.2
  • 2
    • 0037154982 scopus 로고    scopus 로고
    • A unified theory of gene expression
    • Orphanides, G., and Reinberg, D. (2002) A unified theory of gene expression, Cell 108, 439–451.
    • (2002) Cell , vol.108 , pp. 439-451
    • Orphanides, G.1    Reinberg, D.2
  • 4
    • 60149093432 scopus 로고    scopus 로고
    • RNA and disease
    • Cooper, T. A., Wan, L., and Dreyfuss, G. (2009) RNA and disease, Cell 136, 777–793.
    • (2009) Cell , vol.136 , pp. 777-793
    • Cooper, T.A.1    Wan, L.2    Dreyfuss, G.3
  • 5
    • 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, 1514–1518.
    • (2005) Science , vol.309 , pp. 1514-1518
    • Moore, M.J.1
  • 6
    • 0036529621 scopus 로고    scopus 로고
    • Comparative genomics and evolution of proteins involved in RNA metabolism
    • Anantharaman, V., Koonin, E. V., and Aravind, L. (2002) Comparative genomics and evolution of proteins involved in RNA metabolism, Nucleic Acids Res 30, 1427–1464.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1427-1464
    • Anantharaman, V.1    Koonin, E.V.2    Aravind, L.3
  • 7
    • 38349169664 scopus 로고    scopus 로고
    • Mechanisms of post– transcriptional regulation by microRNAs: Are the answers in sight?
    • Filipowicz, W., Bhattacharyya, S. N., and Sonenberg, N. (2008) Mechanisms of post– transcriptional regulation by microRNAs: are the answers in sight?, Nat Rev Genet 9, 102–114.
    • (2008) Nat Rev Genet , vol.9 , pp. 102-114
    • Filipowicz, W.1    Bhattacharyya, S.N.2    Sonenberg, N.3
  • 9
    • 40449138572 scopus 로고    scopus 로고
    • Post-transcriptional gene regulation: From genome-wide studies to principles
    • Halbeisen, R. E., Galgano, A., Scherrer, T., and Gerber, A. P. (2008) Post-transcriptional gene regulation: from genome-wide studies to principles, Cell Mol Life Sci 65, 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
  • 10
    • 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, 14085–14090.
    • (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
  • 11
    • 0037313537 scopus 로고    scopus 로고
    • Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
    • Hieronymus, H., and Silver, P. A. (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery, Nat Genet 33, 155–161.
    • (2003) Nat Genet , vol.33 , pp. 155-161
    • Hieronymus, H.1    Silver, P.A.2
  • 12
    • 0347717583 scopus 로고    scopus 로고
    • Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs
    • Inada, M., and Guthrie, C. (2004) Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs, Proc Natl Acad Sci USA 101, 434–439.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 434-439
    • Inada, M.1    Guthrie, C.2
  • 13
    • 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., and Brown, P. O. (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast, PLoS Biol 2, E79.
    • (2004) Plos Biol , vol.2 , pp. E79
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 14
    • 54949148332 scopus 로고    scopus 로고
    • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    • Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., and Brown, P. O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system, PLoS Biol 6, e255.
    • (2008) Plos Biol , vol.6 , pp. e255
    • Hogan, D.J.1    Riordan, D.P.2    Gerber, A.P.3    Herschlag, D.4    Brown, P.O.5
  • 15
    • 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., and Herschlag, D. (2006) Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster, Proc Natl Acad Sci USA 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
  • 16
    • 0037194732 scopus 로고    scopus 로고
    • Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans
    • Roy, P. J., Stuart, J. M., Lund, J., and Kim, S. K. (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans, Nature 418, 975–979.
    • (2002) Nature , vol.418 , pp. 975-979
    • Roy, P.J.1    Stuart, J.M.2    Lund, J.3    Kim, S.K.4
  • 17
    • 31544432771 scopus 로고    scopus 로고
    • RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5’ region of mRNAs whose translation it activates
    • Schmitz-Linneweber, C., Williams-Carrier, R., and Barkan, A. (2005) RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5’ region of mRNAs whose translation it activates, Plant Cell 17, 2791–2804.
    • (2005) Plant Cell , vol.17 , pp. 2791-2804
    • Schmitz-Linneweber, C.1    Williams-Carrier, R.2    Barkan, A.3
  • 19
    • 2142806748 scopus 로고    scopus 로고
    • Gene expression analysis of messenger RNP complexes
    • Penalva, L. O., Tenenbaum, S. A., and Keene, J. D. (2004) Gene expression analysis of messenger RNP complexes, Methods Mol Biol 257, 125–134.
    • (2004) Methods Mol Biol , vol.257 , pp. 125-134
    • Penalva, L.O.1    Tenenbaum, S.A.2    Keene, J.D.3
  • 21
    • 33749262968 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein
    • Townley-Tilson, W. H., Pendergrass, S. A., Marzluff, W. F., and Whitfield, M. L. (2006) Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein, RNA 12, 1853–1867.
    • (2006) RNA , vol.12 , pp. 1853-1867
    • Townley-Tilson, W.H.1    Pendergrass, S.A.2    Marzluff, W.F.3    Whitfield, M.L.4
  • 22
    • 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., and Keene, J. D. (2008) Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets, Mol Cell Biol 28, 4093–4103.
    • (2008) Mol Cell Biol , vol.28 , pp. 4093-4103
    • Morris, A.R.1    Mukherjee, N.2    Keene, J.D.3
  • 23
    • 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., and Gerber, A. P. (2008) Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system, PLoS One 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
  • 24
    • 78649741223 scopus 로고    scopus 로고
    • Systematic analysis of posttranscriptional gene expression
    • Morris, A. R., Mukherjee, N., and Keene, J. D. (2009) Systematic analysis of posttranscriptional gene expression, WIREs Syst Biol Med, DOI: 10.1002/wsbm.54
    • (2009) Wires Syst Biol Med
    • Morris, A.R.1    Mukherjee, N.2    Keene, J.D.3
  • 25
    • 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, 341–344.
    • (2000) Science , vol.290 , pp. 341-344
    • Takizawa, P.A.1    Derisi, J.L.2    Wilhelm, J.E.3    Vale, R.D.4
  • 26
  • 27
    • 70349671210 scopus 로고    scopus 로고
    • An RNA transport system in Candida albicans regulates hyphal morphology and invasive growth
    • Elson, S. L., Noble, S. M., Solis, N. V., Filler, S. G., and Johnson, A. D. (2009) An RNA transport system in Candida albicans regulates hyphal morphology and invasive growth, PLoS Genet 5, e1000664.
    • (2009) Plos Genet , vol.5
    • Elson, S.L.1    Noble, S.M.2    Solis, N.V.3    Filler, S.G.4    Johnson, A.D.5
  • 28
    • 24044552183 scopus 로고    scopus 로고
    • Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails
    • Kunitomo, H., Uesugi, H., Kohara, Y., and Iino, Y. (2005) Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails, Genome Biol 6, R17.
    • (2005) Genome Biol , vol.6 , pp. R17
    • Kunitomo, H.1    Uesugi, H.2    Kohara, Y.3    Iino, Y.4
  • 29
    • 13644250272 scopus 로고    scopus 로고
    • RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells
    • Penalva, L. O., Burdick, M. D., Lin, S. M., Sutterluety, H., and Keene, J. D. (2004) RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells, Mol Cancer 3, 24.
    • (2004) Mol Cancer , vol.3 , pp. 24
    • Penalva, L.O.1    Burdick, M.D.2    Lin, S.M.3    Sutterluety, H.4    Keene, J.D.5
  • 31
    • 65249176527 scopus 로고    scopus 로고
    • Stress-Dependent Coordination of Transcriptome and Translatome in Yeast
    • Halbeisen, R. E., and Gerber, A. P. (2009) Stress-Dependent Coordination of Transcriptome and Translatome in Yeast, PLoS Biol 7, e105.
    • (2009) Plos Biol , vol.7 , pp. e105
    • Halbeisen, R.E.1    Gerber, A.P.2
  • 33
    • 37649021046 scopus 로고    scopus 로고
    • Identification of human microRNA targets from isolated argonaute protein complexes
    • Beitzinger, M., Peters, L., Zhu, J. Y., Kremmer, E., and Meister, G. (2007) Identification of human microRNA targets from isolated argonaute protein complexes, RNA Biol 4, 76–84.
    • (2007) RNA Biol , vol.4 , pp. 76-84
    • Beitzinger, M.1    Peters, L.2    Zhu, J.Y.3    Kremmer, E.4    Meister, G.5
  • 34
    • 47749154078 scopus 로고    scopus 로고
    • Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance
    • Hendrickson, D. G., Hogan, D. J., Herschlag, D., Ferrell, J. E., and Brown, P. O. (2008) Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance, PLoS One 3, e2126.
    • (2008) Plos One , vol.3
    • Hendrickson, D.G.1    Hogan, D.J.2    Herschlag, D.3    Ferrell, J.E.4    Brown, P.O.5
  • 36
  • 37
    • 70350038073 scopus 로고    scopus 로고
    • Systematic analysis of dynamic miRNA-target interactions during C. elegans development
    • Zhang, L., Hammell, M., Kudlow, B. A., Ambros, V., and Han, M. (2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development, Development 136, 3043–3055.
    • (2009) Development , vol.136 , pp. 3043-3055
    • Zhang, L.1    Hammell, M.2    Kudlow, B.A.3    Ambros, V.4    Han, M.5
  • 39
    • 7044272280 scopus 로고    scopus 로고
    • Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
    • Mili, S., and Steitz, J. A. (2004) Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses, RNA 10, 1692–1694.
    • (2004) RNA , vol.10 , pp. 1692-1694
    • Mili, S.1    Steitz, J.A.2
  • 40
    • 42949149690 scopus 로고    scopus 로고
    • Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling
    • Baroni, T. E., Chittur, S. V., George, A. D., and Tenenbaum, S. A. (2008) Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling, Methods Mol Biol 419, 93–108.
    • (2008) Methods Mol Biol , vol.419 , pp. 93-108
    • Baroni, T.E.1    Chittur, S.V.2    George, A.D.3    Tenenbaum, S.A.4
  • 42
    • 0242497663 scopus 로고    scopus 로고
    • CLIP identifies Nova-regulated RNA networks in the brain
    • Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., and Darnell, R. B. (2003) CLIP identifies Nova-regulated RNA networks in the brain, Science 302, 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
  • 43
    • 27944508215 scopus 로고    scopus 로고
    • CLIP: A method for identifying protein-RNA interaction sites in living cells
    • Ule, J., Jensen, K., Mele, A., and Darnell, R. B. (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells, Methods 37, 376–386.
    • (2005) Methods , vol.37 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 44
    • 84934437354 scopus 로고    scopus 로고
    • CLIP: Crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins
    • Jensen, K. B., and Darnell, R. B. (2008) CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins, Methods Mol Biol 488, 85–98.
    • (2008) Methods Mol Biol , vol.488 , pp. 85-98
    • Jensen, K.B.1    Darnell, R.B.2
  • 45
    • 59649107040 scopus 로고    scopus 로고
    • An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    • Yeo, G. W., Coufal, N. G., Liang, T. Y., Peng, G. E., Fu, X. D., and Gage, F. H. (2009) An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells, Nat Struct Mol Biol 16, 130–137.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 130-137
    • Yeo, G.W.1    Coufal, N.G.2    Liang, T.Y.3    Peng, G.E.4    Fu, X.D.5    Gage, F.H.6
  • 46
    • 67649840910 scopus 로고    scopus 로고
    • CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo
    • Wang, Z., Tollervey, J., Briese, M., Turner, D., and Ule, J. (2009) CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo, Methods 48, 287–293.
    • (2009) Methods , vol.48 , pp. 287-293
    • Wang, Z.1    Tollervey, J.2    Briese, M.3    Turner, D.4    Ule, J.5
  • 47
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi, S. W., Zang, J. B., Mele, A., and Darnell, R. B. (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps, Nature 460, 479–486.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 48
    • 58149300223 scopus 로고    scopus 로고
    • A novel class of mRNA-containing cytoplasmic granules are produced in response to UV-irradiation
    • Gaillard, H., and Aguilera, A. (2008) A novel class of mRNA-containing cytoplasmic granules are produced in response to UV-irradiation, Mol Biol Cell 19, 4980–4992.
    • (2008) Mol Biol Cell , vol.19 , pp. 4980-4992
    • Gaillard, H.1    Aguilera, A.2
  • 49
    • 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, 1161–1167.
    • (2002) Mol Cell , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 50
    • 48249086491 scopus 로고    scopus 로고
    • Biological clocks and the coordination theory of RNA operons and reg-ulons
    • Keene, J. D. (2007) Biological clocks and the coordination theory of RNA operons and reg-ulons, Cold Spring Harb Symp Quant Biol 72, 157–165.
    • (2007) Cold Spring Harb Symp Quant Biol , vol.72 , pp. 157-165
    • Keene, J.D.1
  • 52
    • 73949090104 scopus 로고    scopus 로고
    • Applications of Ultra-high-Throughput Sequencing
    • Fox, S., Filichkin, S., and Mockler, T. C. (2009) Applications of Ultra-high-Throughput Sequencing, Methods Mol Biol 553, 79–108.
    • (2009) Methods Mol Biol , vol.553 , pp. 79-108
    • Fox, S.1    Filichkin, S.2    Mockler, T.C.3
  • 54
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response, Proc Natl Acad Sci USA 98, 5116–5121.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 56
    • 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 Protoc 1, 302–307.
    • (2006) Nat Protoc , vol.1 , pp. 302-307
    • Keene, J.D.1    Komisarow, J.M.2    Friedersdorf, M.B.3
  • 57
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
    • Baldi, P., and Long, A. D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes, Bioinformatics 17, 509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2


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