Post-transcriptional gene regulation: From genome-wide studies to principles

Cellular and Molecular Life Sciences

Volumn 65, Issue 5, 2008, Pages 798-813

  Halbeisen, R E ^a   Galgano, A ^a   Scherrer, T ^a   Gerber, A P ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

DNA microarray; Post transcriptional gene regulation; RNA binding protein; Systems biology; Translation

Indexed keywords

MESSENGER RNA; RNA BINDING PROTEIN; UNTRANSLATED RNA;

GENE CONTROL; GENE EXPRESSION; GENOME ANALYSIS; HUMAN; NONHUMAN; PHYSIOLOGY; PROTEIN RNA BINDING; RATING SCALE; REGULATORY MECHANISM; REVIEW; RNA SEQUENCE; RNA STRUCTURE; TRANSLATION REGULATION;

GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA PROCESSING, POST-TRANSCRIPTIONAL; TRANSCRIPTION, GENETIC;

EID: 40449138572     PISSN: 1420682X     EISSN: 15691632     Source Type: Journal    
DOI: 10.1007/s00018-007-7447-6     Document Type: Review

References (119)

1. Orphanides, G. and Reinberg, D. (2002) A unified theory of gene expression. Cell 108, 439-451.
2. Maniatis, T. and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature 416, 499-506.
3. 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.
4. Moore, M. J. (2005) From birth to death: The complex lives of eukaryotic mRNAs. Science 309, 1514-1518.
5. St Johnston, D. (2005) Moving messages: The intracellular localization of mRNAs. Nat. Rev. Mol. Cell. Biol. 6, 363-375.
6. Gebauer, F. and Hentze, M. W. (2004) Molecular mechanisms of translational control. Nat. Rev. Mol. Cell. Biol. 5, 827-835.
7. Parker, R. and Song, H. (2004) The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11, 121-127.
8. Jensen, O. N. (2006) Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell. Biol. 7, 391-403.
9. Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E. and Young, R. A. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104.
10. Lee, T. I. Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., Zeitlinger, J., Jennings, E. G., Murray, H. L., Gordon, D. B., Ren, B., Wyrick, J. J., Tagne, J. B., Volkert, T. L., Fraenkel, E., Gifford, D. K. and Young, R. A. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
11. Ihmels, J., Bergmann, S., Gerami-Nejad, M., Yanai, I., McClellan, M., Berman, J. and Barkai, N. (2005) Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309, 938-940.
12. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31, 370-377.
13. Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166-176.
14. Hieronymus, H. and Silver, P. A. (2004) A systems view of mRNP biology. Genes Dev. 18, 2845-2860.
15. Mata, J., Marguerat, S. and Bahler, J. (2005) Post-transcriptional control of gene expression: A genome-wide perspective. Trends Biochem. Sci. 30, 506-514.
16. Keene, J. D. (2007) RNA regulons: Coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533-543.
17. Czaplinski, K. and Singer, R. H. (2006) Pathways for mRNA localization in the cytoplasm. Trends Biochem. Sci. 31, 687-693.
18. Diehn, M., Eisen, M. B., Botstein, D. and Brown, P. O. (2000) Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat. Genet. 25, 58-62.
19. de Jong, M., van Breukelen, B., Wittink, F. R., Menke, F. L., Weisbeek, P. J. and Van den Ackerveken, G. (2006) Membrane-associated transcripts in Arabidopsis; their isolation and characterization by DNA microarray analysis and bioinformatics. Plant J. 46, 708-721.
20. Diehn, M., Bhattacharya, R., Botstein, D. and Brown, P. O. (2006) Genome-scale identification of membrane-associated human mRNAs. PLoS Genet. 2, e11.
21. Corral-Debrinski, M., Blugeon, C. and Jacq, C. (2000) In yeast, the 3′ untranslated region or the presequence of ATM1 is required for the exclusive localization of its mRNA to the vicinity of mitochondria. Mol. Cell. Biol. 20, 7881-7892.
22. Marc, P., Margeot, A., Devaux, F., Blugeon, C., Corral-Debrinski, M. and Jacq, C. (2002) Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBORep. 3, 159-164.
23. Sylvestre, J., Vialette, S., Corral Debrinski, M. and Jacq, C. (2003) Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria. Genome Biol. 4, R44.
24. Brock, A., Huang, S. and Ingber, D. E. (2003) Identification of a distinct class of cytoskeleton-associated mRNAs using microarray technology. BMC Cell Biol. 4, 6.
25. Russo, A., Russo, G., Cuccurese, M., Garbi, C. and Pietropaolo, C. (2006) The 3′-untranslated region directs ribosomal protein-encoding mRNAs to specific cytoplasmic regions. Biochim. Biophys. Acta 1763, 833-843.
26. Martin, K. C. and Zukin, R. S. (2006) RNA trafficking and local protein synthesis in dendrites: An overview. J. Neurosci. 26, 7131-7134.
27. Kiebler, M. A. and Bassell, G. J. (2006) Neuronal RNA granules: Movers and makers. Neuron 51, 685-690.
28. Matsumoto, M., Setou, M. and Inokuchi, K. (2007) Transcriptome analysis reveals the population of dendritic RNAs and their redistribution by neural activity. Neurosci. Res. 57, 411-423.
29. Muller, M., Heuck, A. and Niessing, D. (2007) Directional mRNA transport in eukaryotes: Lessons from yeast. Cell. Mol. Life Sci. 64, 171-180.
30. Hirokawa, N. (2006) mRNA transport in dendrites: RNA granules, motors, and tracks. J. Neurosci. 26, 7139-7142.
31. Brown, V. Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., Darnell, R. B. and Warren, S. T. (2001) Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107, 477-487.
32. 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, 191-198.
33. 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.
34. 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.
35. Rajasekhar, V. K. and Holland, E. C. (2004) Postgenomic global analysis of translational control induced by oncogenic signaling. Oncogene 23, 3248-3264.
36. Klann, E. and Dever, T. E. (2004) Biochemical mechanisms for translational regulation in synaptic plasticity. Nat. Rev. Neurosci. 5, 931-942.
37. Bilanges, B. and Stokoe, D. (2007) Mechanisms of translational deregulation in human tumors and therapeutic intervention strategies. Oncogene 26, 5973-5990.
38. Lu, P., Vogel, C., Wang, R., Yao, X. and Marcotte, E. M. (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25, 117-124.
39. Brockmann, R., Beyer, A., Heinisch, J. J. and Wilhelm, T. (2007) Posttranscriptional expression regulation: What determines translation rates? PLoS Comput. Biol. 3, e57.
40. Qin, X. and Sarnow, P. (2004) Preferential translation of internal ribosome entry site-containing mRNAs during the mitotic cycle in mammalian cells. J. Biol. Chem. 279, 13721-13728.
41. Richter, J. D. and Sonenberg, N. (2005) Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433, 477-480.
42. Kuersten, S. and Goodwin, E. B. (2003) The power of the 3′ UTR: Translational control and development. Nat. Rev. Genet. 4, 626-637.
43. Eisenstein, R. S. and Ross, K. L. (2003) Novel roles for iron regulatory proteins in the adaptive response to iron deficiency. J. Nutr. 133, 1510S-1516S.
44. Pillai, R. S., Bhattacharyya, S. N. and Filipowicz, W. (2007) Repression of protein synthesis by miRNAs: How many mechanisms? Trends Cell Biol. 17, 118-126.
45. Bhattacharyya, S. N., Habermacher, R., Martine, U., Closs, E. I. and Filipowicz, W. (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125, 1111-1124.
46. Beilharz, T. H. and Preiss, T. (2004) Translational profiling: The genome-wide measure of the nascent proteome. Brief Funct. Genomic. Proteomic. 3, 103-111.
47. Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O. and Herschlag, D. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 3889-3894.
48. Lackner, D. H., Beilharz, T. H., Marguerat, S., Mata, J., Watt, S., Schubert, F., Preiss, T. and Bahler, J. (2007) A network of multiple regulatory layers shapes gene expression in fission yeast. Mol. Cell 26, 145-155.
49. Qin, X., Ahn, S., Speed, T. P. and Rubin, G. M. (2007) Global analyses of mRNA translational control during early Drosophila embryogenesis. Genome Biol. 8, R63.
50. Beilharz, T. H. and Preiss, T. (2007) Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA 13, 982-997.
51. Hurowitz, E. H. and Brown, P. O. (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol. 5, R2.
52. Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D. and Brown, P. O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99, 5860-5865.
53. Kuhn, K. M., DeRisi, J. L., Brown, P. O. and Sarnow, P. (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21, 916-927.
54. Preiss, T., Baron-Benhamou, J., Ansorge, W. and Hentze, M. W. (2003) Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat. Struct. Biol. 10, 1039-1047.
55. Smirnova, J. B., Selley, J. N., Sanchez-Cabo, F., Carroll, K., Eddy, A. A., McCarthy, J. E., Hubbard, S. J., Pavitt, G. D., Grant, C. M. and Ashe, M. P. (2005) Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol. Cell. Biol. 25, 9340-9349.
56. Shenton, D., Smirnova, J. B., Selley, J. N., Carroll, K., Hubbard, S. J., Pavitt, G. D., Ashe, M. P. and Grant, C. M. (2006) Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J. Biol. Chem. 281, 29011-29021.
57. Rudra, D. and Warner, J. R. (2004) What better measure than ribosome synthesis? Genes Dev. 18, 2431-2436.
58. Johannes, G., Carter, M. S., Eisen, M. B., Brown, P. O. and Sarnow, P. (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. USA 96, 13118-13123.
59. Zong, Q., Schummer, M., Hood, L. and Morris, D. R. (1999) Messenger RNA translation state: The second dimension of high-throughput expression screening. Proc. Natl. Acad. Sci. USA 96, 10632-10636.
60. Rajasekhar, V. K., Viale, A., Socci, N. D., Wiedmann, M., Hu, X. and Holland, E. C. (2003) Oncogenic Ras and Akt signaling contribute to glioblastoma formation by differential recruitment of existing mRNAs to polysomes. Mol. Cell 12, 889-901.
61. Provenzani, A., Fronza, R., Loreni, F., Pascale, A., Amadio, M. and Quattrone, A. (2006) Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis. Carcinogenesis 27, 1323-1333.
62. Mamane, Y., Petroulakis, E., Martineau, Y., Sato, T. A., Larsson, O., Rajasekhar, V. K. and Sonenberg, N. (2007) Epigenetic activation of a subset of mRNAs by eIF4E explains its effects on cell proliferation. PLoS ONE 2, e242.
63. Lu, X., de la Pena, L., Barker, C., Camphausen, K. and Tofilon, P. J. (2006) Radiation-induced changes in gene expression involve recruitment of existing messenger RNAs to and away from polysomes. Cancer Res. 66, 1052-1061.
64. Greenman, I. C., Gomez, E., Moore, C. E. and Herbert, T. P. (2007) Distinct glucose-dependent stress responses revealed by translational profiling in pancreatic beta-cells. J. Endocrinol. 192, 179-187.
65. Thomas, J. D. and Johannes, G. J. (2007) Identification of mRNAs that continue to associate with polysomes during hypoxia. RNA 13, 1116-1131.
66. Condon, C. (2007) Maturation and degradation of RNA in bacteria. Curr. Opin. Microbiol. 10, 271-278.
67. Raghavan, A. and Bohjanen, P. R. (2004) Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression. Brief. Funct. Genomic. Proteomic. 3, 112-124.
68. Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S. and Cohen, S. N. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99, 9697-9702.
69. Selinger, D. W., Saxena, R. M., Cheung, K. J., Church, G. M. and Rosenow, C. (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13, 216-223.
70. Hambraeus, G., von Wachenfeldt, C. and Hederstedt, L. (2003) Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol. Genet. Genomics 269, 706-714.
71. Andersson, A. F., Lundgren, M., Eriksson, S., Rosenlund, M., Bernander, R. and Nilsson, P. (2006) Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol. 7, R99.
72. Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. D. and Hughes, T. R. (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol. Cell. Biol. 24, 5534-5547.
73. Gutierrez, R. A., Ewing, R. M., Cherry, J. M. and Green, P. J. (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl. Acad. Sci. USA 99, 11513-11518.
74. Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., Magnasco, M. and Darnell, J. E. Jr. (2003) Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes. Genome Res. 13, 1863-1872.
75. Bernstein, J. A., Lin, P. H., Cohen, S. N. and Lin-Chao, S. (2004) Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. USA 101, 2758-2763.
76. Barnett, T. C., Bugrysheva, J. V. and Scott, J. R. (2007) Role of mRNA stability in growth phase regulation of gene expression in the group A streptococcus. J. Bacteriol. 189, 1866-1873.
77. He, F., Li, X., Spatrick, P., Casillo, R., Dong, S. and Jacobson, A. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12, 1439-1452.
78. Guan, Q., Zheng, W., Tang, S., Liu, X., Zinkel, R. A., Tsui, K. W., Yandell, B. S. and Culbertson, M. R. (2006) Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2, e203.
79. Houalla, R., Devaux, F., Fatica, A., Kufel, J., Barrass, D., Torchet, C. and Tollervey, D. (2006) Microarray detection of novel nuclear RNA substrates for the exosome. Yeast 23, 439-454.
80. 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.
81. 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.
82. Foat, B. C., Houshmandi, S. S., Olivas, W. M. and Bussemaker, H. J. (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl. Acad. Sci. USA 102, 17675-17680.
83. Raghavan, A., Ogilvie, R. L., Reilly, C., Abelson, M. L., Raghavan, S., Vasdewani, J., Krathwohl, M. and Bohjanen, P. R. (2002) Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res. 30, 5529-5538.
84. Su, Y. Q., Sugiura, K., Woo, Y., Wigglesworth, K., Kamdar, S., Affourtit, J. and Eppig, J. J. (2007) Selective degradation of transcripts during meiotic maturation of mouse oocytes. Dev. Biol. 302, 104-117.
85. Raghavan, A., Dhalla, M., Bakheet, T., Ogilvie, R. L., Vlasova, I. A., Khabar, K. S., Williams, B. R. and Bohjanen, P. R. (2004) Patterns of coordinate down-regulation of ARE-containing transcripts following immune cell activation. Genomics 84, 1002-1013.
86. Lai, W. S., Parker, J. S., Grissom, S. F., Stumpo, D. J. and Blackshear, P. J. (2006) Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. Mol. Cell. Biol. 26, 9196-9208.
87. 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.
88. Hollien, J. and Weissman, J. S. (2006) Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. Science 313, 104-107.
89. Lin, W. J., Duffy, A. and Chen, C. Y. (2007) Localization of AU-rich element-containing mRNA in cytoplasmic granules containing exosome subunits. J. Biol. Chem. 282, 19958-19968.
90. 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.
91. 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.
92. Keene, J. D. and Tenenbaum, S. A. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 9, 1161-1167.
93. 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.
94. Wickens, M., Bernstein, D. S., Kimble, J. and Parker, R. (2002) A PUF family portrait: 3′UTR regulation as a way of life. Trends Genet. 18, 150-157.
95. Kim 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.
96. 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. 28 June, 4(2) Epub ahead of print.
97. Easow, G., Teleman, A. A. and Cohen, S. M. (2007) Isolation of microRNA targets by miRNP immunopurification. RNA 13, 1198-1204.
98. 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.
99. 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.
100. Yang, Z., Edenberg, H. J. and Davis, R. L. (2005) Isolation of mRNA from specific tissues of Drosophila by mRNA tagging. Nucleic Acids Res. 33, e148.
101. 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.
102. Inada, T., Winstall, E., Tarun, S. Z., Jr., Yates, J. R. 3rd, Schieltz, D. and Sachs, A. B. (2002) One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs. RNA 8, 948-958.
103. 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.
104. Valencia-Sanchez, M. A., Liu, J., Hannon, G. J. and Parker, R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20, 515-524.
105. Audic, Y. and Hartley, R. S. (2004) Post-transcriptional regulation in cancer. Biol. Cell 96, 479-498.
106. 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.
107. Li, A. M., Watson, A. and Fridovich-Keil, J. L. (2003) Scp160p associates with specific mRNAs in yeast. Nucleic Acids Res. 31, 1830-1837.
108. 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.
109. Puig, S., Askeland, E. and Thiele, D. J. (2005) Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell 120, 99 -110.
110. Lopez de Silanes, I., Zhan, M., Lal, A., Yang, X. and Gorospe, M. (2004) Identification of a target RNA motif for RNA-binding protein HuR. Proc. Natl. Acad. Sci. USA 101, 2987-2992.
111. 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.
112. Liu, W., Seto, J., Sibille, E. and Toth, M. (2003) The RNA binding domain of Jerky consists of tandemly arranged helix-turn-helix/homeodomain-like motifs and binds specific sets of mRNAs. Mol. Cell. Biol. 23, 4083-4093.
113. Waggoner, S. A. and Liebhaber, S. A. (2003) Identification of mRNAs associated with alphaCP2-containing RNP complexes. Mol. Cell. Biol. 23, 7055-7067.
114. 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.
115. 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.
116. Tanaka, T. S., Lopez de Silanes, I., Sharova, L. V., Akutsu, H., Yoshikawa, T., Amano, H., Yamanaka, S., Gorospe, M. and Ko, M. S. (2006) Esg1, expressed exclusively in preimplantation embryos, germline, and embryonic stem cells, is a putative RNA-binding protein with broad RNA targets. Dev. Growth Differ. 48, 381-390.
117. 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.
118. 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.
119. 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.