Genome-Wide Analysis of RNA-Protein Interactions in Plants

  • Alice Barkan
Part of the Methods in Molecular Biology™ book series (MIMB, volume 553)


RNA–protein interactions profoundly impact organismal development and function through their contributions to the basal gene expression machineries and their regulation of post-transcriptional processes. The repertoire of predicted RNA binding proteins (RBPs) in plants is particularly large, suggesting that the RNA–protein interactome in plants may be more complex and dynamic even than that in metazoa. To dissect RNA–protein interaction networks, it is necessary to identify the RNAs with which each RBP interacts and to determine how those interactions influence RNA fate and downstream processes. Identification of the native RNA ligands of RBPs remains a challenge, but several high-throughput methods for the analysis of RNAs that copurify with specific RBPs from cell extract have been reported recently. This chapter reviews approaches for defining the native RNA ligands of RBPs on a genome-wide scale and provides a protocol for a method that has been used to this end for RBPs that localize to the chloroplast.

Key words

RNA–protein interaction RIP-chip RNA coimmunoprecipitation microarray RNA binding protein 



I would like to thank Rosalind Williams-Carrier and Christian Schmitz-Linneweber for their central contributions in developing our RIP-chip methodology, Eric Johnson and his laboratory for guidance in microarray printing and hybridization, and Jana Prikryl, Yukari Asakura, Susan Belcher, and Kenneth Watkins for optimizing aspects of the protocols. I would also like to thank Rodger Voelker, Todd Mockler, and Don Rio for stimulating discussions and for their comments on the manuscript and Don Rio for communicating results prior to publication. This work was supported by grant DBI-0421799 from the National Science Foundation.


  1. 1.
    Hieronymus, H. and Silver, P.A. (2004) A systems view of mRNP biology. Genes Dev. 18, 2845–2860.PubMedCrossRefGoogle Scholar
  2. 2.
    Keene, J.D. (2007) RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533–543.PubMedCrossRefGoogle Scholar
  3. 3.
    Jambhekar, A. and Derisi, J.L. (2007) Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA. 13, 625–642.PubMedCrossRefGoogle Scholar
  4. 4.
    Okita, T.W. and Choi, S.B. (2002) mRNA localization in plants: targeting to the cell's cortical region and beyond. Curr. Opin. Plant Biol. 5, 553–559.PubMedCrossRefGoogle Scholar
  5. 5.
    Knoop, V. and Brennicke, A. (2002) Molecular biology of the plant mitochondrion. Crit. Rev. Plant Sci. 21, 111–126.CrossRefGoogle Scholar
  6. 6.
    Bollenbach, T.J., Schuster, G., and Stern, D.B. (2004) Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover. Prog. Nucleic Acid Res. Mol. Biol. 78, 305–337.PubMedCrossRefGoogle Scholar
  7. 7.
    Bonen, L. (2004) in Molecular Biology and Biotechnology of Plant Organelles, eds. Daniell, H. & Chase, C. (Springer, Dordrecht), pp. 323–345.Google Scholar
  8. 8.
    Barkan, A. (2004) in Molecular Biology and Biotechnology of Plant Organelles, eds. Daniell, H. & Chase, C. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 281–308.Google Scholar
  9. 9.
    Zerges, W. (2004) in Molecular Biology and Biotechnology of Plant Organelles, eds. Daniell, H. & Chase, C. (Springer, Dordrecht), pp. 347–383.Google Scholar
  10. 10.
    Belostotsky, D.A. and Rose, A.B. (2005) Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events. Trends Plant Sci. 10, 347–353.PubMedCrossRefGoogle Scholar
  11. 11.
    Fedoroff, N. (2002) RNA-binding proteins in plants: the tip of an iceberg? Plant J. 5, 452–459.Google Scholar
  12. 12.
    Carrington, J. and Ambros, V. (2003) Role of MicroRNAs in plant and animal development. Science. 301, 336–338.PubMedCrossRefGoogle Scholar
  13. 13.
    Kuhn, J. and Schroeder, J. (2003) Impacts of altered RNA metabolism on abscisic acid signalling. Curr. Opin. Plant Biol. 6, 463–469.PubMedCrossRefGoogle Scholar
  14. 14.
    Lidder, P., Gutierrez, R.A., Salome, P.A., McClung, C.R., and Green, P.J. (2005) Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. Plant Physiol. 138, 2374–2385.PubMedCrossRefGoogle Scholar
  15. 15.
    Kawaguchi, R., Girke, T., Bray, E.A., and Bailey-Serres, J. (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J. 38, 823–839.PubMedCrossRefGoogle Scholar
  16. 16.
    Branco-Price, C., Kawaguchi, R., Ferreira, R.B., and Bailey-Serres, J. (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann. Bot. (Lond). 96, 647–660.CrossRefGoogle Scholar
  17. 17.
    Reddy, A.S. (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 58, 267–294.PubMedCrossRefGoogle Scholar
  18. 18.
    Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A., and Shinozaki, K. (2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 32, 5096–5103.PubMedCrossRefGoogle Scholar
  19. 19.
    Wang, B.B. and Brendel, V. (2006) Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA. 103, 7175–7180.Google Scholar
  20. 20.
    Dreyfuss, G., Kim, V.N., and Kataoka, N. (2002) Messenger-RNA-binding proteins and the messages they carry. Nat. Rev. Mol. Cell. Biol. 3, 195–205.PubMedCrossRefGoogle Scholar
  21. 21.
    Wang, B.B. and Brendel, V. (2004) The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 5, R102.PubMedCrossRefGoogle Scholar
  22. 22.
    Belostotsky, D. (2003) Unexpected complexity of poly(A)-binding protein gene families in flowering plants: three conserved lineages that are at least 200 million years old and possible auto- and cross-regulation. Genetics. 163, 311–319.PubMedGoogle Scholar
  23. 23.
    Lorkovic, Z. and Barta, A. (2002) Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Res. 30, 623–635.PubMedCrossRefGoogle Scholar
  24. 24.
    Barkan, A., Klipcan, L., Ostersetzer, O., Kawamura, T., Asakura, Y., and Watkins, K. (2007) The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. RNA. 13, 55–64.PubMedCrossRefGoogle Scholar
  25. 25.
    Lurin, C., Andres, C., Aubourg, S., Bellaoui, M., Bitton, F., Bruyere, C., Caboche, M., Debast, C., Gualberto, J., Hoffmann, B., Lecharny, A., Le Ret, M., Martin-Magniette, M. L., Mireau, H., Peeters, N., Renou, J.P., Szurek, B., Taconnat, L., and Small, I. (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 16, 2089–2103.PubMedCrossRefGoogle Scholar
  26. 26.
    Walker, N.S., Stiffler, N., and Barkan, A. (2007) POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Res. 35, D852–D856.PubMedCrossRefGoogle Scholar
  27. 27.
    Small, I. and Peeters, N. (2000) The PPR motif – a TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci. 25, 46–47.PubMedCrossRefGoogle Scholar
  28. 28.
    Blanchette, M., Labourier, E., Green, R.E., Brenner, S.E., and Rio, D.C. (2004) Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Mol. Cell. 14, 775–786.PubMedCrossRefGoogle Scholar
  29. 29.
    Blanchette, M., Green, R.E., Brenner, S.E., and Rio, D.C. (2005) Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 19, 1306–1314.PubMedCrossRefGoogle Scholar
  30. 30.
    Rehwinkel, J., Herold, A., Gari, K., Kocher, T., Rode, M., Ciccarelli, F.L., Wilm, M., and Izaurralde, E. (2004) Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster. Nat. Struct. Mol. Biol. 11, 558–566.PubMedCrossRefGoogle Scholar
  31. 31.
    Fitzwater, T. and Polisky, B. (1996) A SELEX primer. Methods Enzymol. 267, 275–301.PubMedCrossRefGoogle Scholar
  32. 32.
    Kim, S., Shi, H., Lee, D.K., and Lis, J.T. (2003) Specific SR protein-dependent splicing substrates identified through genomic SELEX. Nucleic Acids Res. 31, 1955–1961.PubMedCrossRefGoogle Scholar
  33. 33.
    Faustino, N.A. and Cooper, T.A. (2005) Identification of putative new splicing targets for ETR-3 using sequences identified by systematic evolution of ligands by exponential enrichment. Mol. Cell. Biol. 25, 879–887.PubMedCrossRefGoogle Scholar
  34. 34.
    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, 227–233.PubMedCrossRefGoogle Scholar
  35. 35.
    Seay, D., Hook, B., Evans, K., and Wickens, M. (2006) A three-hybrid screen identifies mRNAs controlled by a regulatory protein. RNA. 12, 1594–1600.PubMedCrossRefGoogle Scholar
  36. 36.
    Miller, J.W., Urbinati, C.R., Teng-Umnuay, P., Stenberg, M.G., Byrne, B.J., Thornton, C.A., and Swanson, M.S. (2000) Recruitment of human muscleblind proteins to (CUG)(n) expansions associated with myotonic dystrophy. EMBO J. 19, 4439–4448.PubMedCrossRefGoogle Scholar
  37. 37.
    Asakura, Y. and Barkan, A. (2007) A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts. Plant Cell. 19, 3864–3875.Google Scholar
  38. 38.
    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.PubMedCrossRefGoogle Scholar
  39. 39.
    Schmitz-Linneweber, C., Williams-Carrier, R.E., Williams-Voelker, P.M., Kroeger, T.S., Vichas, A., and Barkan, A. (2006) A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell. 18, 2650–2663.PubMedCrossRefGoogle Scholar
  40. 40.
    Watkins, K., Kroeger, T., Cooke, A., Williams-Carrier, R., Friso, G., Belcher, S., Wijk, K.V., and Barkan, A. (2007) A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. Plant Cell. 19, 2606–2623.PubMedCrossRefGoogle Scholar
  41. 41.
    Zanetti, M.E., Chang, I.F., Gong, F., Galbraith, D.W., and Bailey-Serres, J. (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol. 138, 624–635.PubMedCrossRefGoogle Scholar
  42. 42.
    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.Google Scholar
  43. 43.
    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.PubMedCrossRefGoogle Scholar
  44. 44.
    Shepard, K.A., Gerber, A.P., Jambhekar, A., Takizawa, P.A., Brown, P.O., Herschlag, D., DeRisi, J.L., and Vale, R.D. (2003) Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc. Natl. Acad. Sci. USA. 100, 11429–11434.Google Scholar
  45. 45.
    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.PubMedCrossRefGoogle Scholar
  46. 46.
    Duttagupta, R., Tian, B., Wilusz, C.J., Khounh, D.T., Soteropoulos, P., Ouyang, M., Dougherty, J.P., and Peltz, S.W. (2005) Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol. Cell. Biol. 25, 5499–5513.PubMedCrossRefGoogle Scholar
  47. 47.
    Kotovic, K.M., Lockshon, D., Boric, L., and Neugebauer, K.M. (2003) Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol. Cell. Biol. 23, 5768–5779.PubMedCrossRefGoogle Scholar
  48. 48.
    Guisbert, K., Duncan, K., Li, H., and Guthrie, C. (2005) Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. RNA. 11, 383–393.CrossRefGoogle Scholar
  49. 49.
    Oeffinger, M., Wei, K.E., Rogers, R., Degrasse, J.A., Chait, B.T., Aitchison, J.D., and Rout, M.P. (2007) Comprehensive analysis of diverse ribonucleoprotein complexes. Nat. Methods. 4, 951–956.PubMedCrossRefGoogle Scholar
  50. 50.
    Gabellini, D., D'Antona, G., Moggio, M., Prelle, A., Zecca, C., Adami, R., Angeletti, B., Ciscato, P., Pellegrino, M.A., Bottinelli, R., Green, M.R., and Tupler, R. (2006) Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1. Nature. 439, 973–977.PubMedGoogle Scholar
  51. 51.
    Gabut, M., Mine, M., Marsac, C., Brivet, M., Tazi, J., and Soret, J. (2005) The SR protein SC35 is responsible for aberrant splicing of the E1alpha pyruvate dehydrogenase mRNA in a case of mental retardation with lactic acidosis. Mol. Cell. Biol. 25, 3286–3294.PubMedCrossRefGoogle Scholar
  52. 52.
    Kalyna, M., Lopato, S., and Barta, A. (2003) Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol. Biol. Cell. 14, 3565–3577.PubMedCrossRefGoogle Scholar
  53. 53.
    Corbeil-Girard, L.P., Klein, A.F., Sasseville, A.M., Lavoie, H., Dicaire, M.J., Saint-Denis, A., Page, M., Duranceau, A., Codere, F., Bouchard, J.P., Karpati, G., Rouleau, G.A., Massie, B., Langelier, Y., and Brais, B. (2005) PABPN1 overexpression leads to upregulation of genes encoding nuclear proteins that are sequestered in oculopharyngeal muscular dystrophy nuclear inclusions. Neurobiol. Dis. 18, 551–567.PubMedCrossRefGoogle Scholar
  54. 54.
    Kiesler, E., Hase, M.E., Brodin, D., and Visa, N. (2005) Hrp59, an hnRNP M protein in Chironomus and Drosophila, binds to exonic splicing enhancers and is required for expression of a subset of mRNAs. J. Cell. Biol. 168, 1013–1025.PubMedCrossRefGoogle Scholar
  55. 55.
    Gama-Carvalho, M., Barbosa-Morais, N.L., Brodsky, A.S., Silver, P.A., and Carmo-Fonseca, M. (2006) Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol. 7, R113.PubMedCrossRefGoogle Scholar
  56. 56.
    Lopez de Silanes, I., Galban, S., Martindale, J.L., Yang, X., Mazan-Mamczarz, K., Indig, F.E., Falco, G., Zhan, M., and Gorospe, M. (2005) Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1. Mol. Cell. Biol. 25, 9520–9531.Google Scholar
  57. 57.
    Brown, V., Jin, P., Ceman, S., Darnell, J., O'Donnell, W., Tenenbaum, S., Jin, X., Feng, U., Wilkinson, K., Keene, J., Darnell, R., and Warren, S. (2001) Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in Fragile X Syndrome. Cell. 107, 477–487.PubMedCrossRefGoogle Scholar
  58. 58.
    Reynolds, N., Collier, B., Maratou, K., Bingham, V., Speed, R.M., Taggart, M., Semple, C.A., Gray, N.K., and Cooke, H.J. (2005) Dazl binds in vivo to specific transcripts and can regulate the pre-meiotic translation of Mvh in germ cells. Hum. Mol. Genet. 14, 3899–3909.PubMedCrossRefGoogle Scholar
  59. 59.
    Tenenbaum, S., Carson, C., Lager, P., and Keene, J. (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl. Acad. Sci. USA. 97, 14085–14090.Google Scholar
  60. 60.
    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.PubMedCrossRefGoogle Scholar
  61. 61.
    Swinburne, I.A., Meyer, C.A., Liu, X.S., Silver, P.A., and Brodsky, A.S. (2006) Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 16, 912–921.PubMedCrossRefGoogle Scholar
  62. 62.
    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.PubMedCrossRefGoogle Scholar
  63. 63.
    Klimek-Tomczak, K., Wyrwicz, L.S., Jain, S., Bomsztyk, K., and Ostrowski, J. (2004) Characterization of hnRNP K protein–RNA interactions. J. Mol. Biol. 342, 1131–1141.PubMedCrossRefGoogle Scholar
  64. 64.
    Eystathioy, T., Chan, E.K., Tenenbaum, S.A., Keene, J.D., Griffith, K., and Fritzler, M.J. (2002) A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol. Biol. Cell. 13, 1338–1351.PubMedCrossRefGoogle Scholar
  65. 65.
    Mordes, D., Yuan, L., Xu, L., Kawada, M., Molday, R.S., and Wu, J.Y. (2007) Identification of photoreceptor genes affected by PRPF31 mutations associated with autosomal dominant retinitis pigmentosa. Neurobiol. Dis. 26, 291–300.PubMedCrossRefGoogle Scholar
  66. 66.
    Guil, S. and Caceres, J.F. (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol. 14, 591–596.PubMedCrossRefGoogle Scholar
  67. 67.
    Waggoner, S.A. and Liebhaber, S.A. (2003) Identification of mRNAs associated with alphaCP2-containing RNP complexes. Mol. Cell. Biol. 23, 7055–7067.PubMedCrossRefGoogle Scholar
  68. 68.
    Labourier, E., Blanchette, M., Feiger, J.W., Adams, M.D., and Rio, D.C. (2002) The KH-type RNA-binding protein PSI is required for Drosophila viability, male fertility, and cellular mRNA processing. Genes Dev. 16, 72–84.PubMedCrossRefGoogle Scholar
  69. 69.
    Zhang, A., Wassarman, K.M., Rosenow, C., Tjaden, B.C., Storz, G., and Gottesman, S. (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50, 1111–1124.PubMedCrossRefGoogle Scholar
  70. 70.
    Easow, G., Teleman, A.A., and Cohen, S.M. (2007) Isolation of microRNA targets by miRNP immunopurification. RNA. 13, 1198–1204.PubMedCrossRefGoogle Scholar
  71. 71.
    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.Google Scholar
  72. 72.
    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.PubMedCrossRefGoogle Scholar
  73. 73.
    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.PubMedCrossRefGoogle Scholar
  74. 74.
    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.PubMedCrossRefGoogle Scholar
  75. 75.
    Niranjanakumari, S., Lasda, E., Brazas, R., and Garcia-Blanco, M.A. (2002) Reversible cross-linking combined with immunoprecipitation to study RNA–protein interactions in vivo. Methods. 26, 182–190.PubMedCrossRefGoogle Scholar
  76. 76.
    Penalva, L.O., Tenenbaum, S.A., and Keene, J.D. (2004) Gene expression analysis of messenger RNP complexes. Methods Mol. Biol. 257, 125–134.PubMedGoogle Scholar
  77. 77.
    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.PubMedCrossRefGoogle Scholar
  78. 78.
    Johnson, D.S., Mortazavi, A., Myers, R.M., and Wold, B. (2007) Genome-wide mapping of in vivo protein–DNA interactions. Science. 316, 1497–1502.PubMedCrossRefGoogle Scholar
  79. 79.
    Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., Thiessen, N., Griffith, O.L., He, A., Marra, M., Snyder, M., and Jones, S. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods. 4, 651–657.PubMedCrossRefGoogle Scholar
  80. 80.
    Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P., Lee, W., Mendenhall, E., O'Donovan, A., Presser, A., Russ, C., Xie, X., Meissner, A., Wernig, M., Jaenisch, R., Nusbaum, C., Lander, E.S., and Bernstein, B.E. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 448, 553–560.PubMedCrossRefGoogle Scholar
  81. 81.
    Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell. 129, 823–837.PubMedCrossRefGoogle Scholar
  82. 82.
    Pinol-Roma, S., Swanson, M.S., Matunis, M.J., and Dreyfuss, G. (1990) Purification and characterization of proteins of heterogeneous nuclear ribonucleoprotein complexes by affinity chromatography. Methods Enzymol. 181, 326–331.PubMedCrossRefGoogle Scholar
  83. 83.
    Haring, M., Offermann, S., Danker, T., Horst, I., Peterhaensel, C., and Stam, M. (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods. 3, 11.PubMedCrossRefGoogle Scholar
  84. 84.
    Barkan, A. (1988) Proteins encoded by a complex chloroplast transcription unit are each translated from both monocistronic and polycistronic mRNAs. EMBO J. 7, 2637–2644.PubMedGoogle Scholar
  85. 85.
    Harlow, E. and Lane, D. (1988) Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor).Google Scholar
  86. 86.
    Barkan, A. (1998) Approaches to investigating nuclear genes that function in chloroplast biogenesis in land plants. Methods Enzymol. 297, 38–57.CrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Alice Barkan
    • 1
  1. 1.Institute of Molecular BiologyUniversity of OregonEugeneUSA

Personalised recommendations