RNA regulons: coordination of post-transcriptional events (original) (raw)

• Orphanides, G. & Reinberg, D. A unified theory of gene expression. Cell 108, 439–451 (2002).
  Article CAS PubMed Google Scholar
• Beckwith, J. The Operon: An Historical Account 1227–1231 (ASM, Washington, 1996).
  Google Scholar
• Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Kosak, S. T. & Groudine, M. Form follows function: the genomic organization of cellular differentiation. Genes Dev. 18, 1371–1384 (2004).
  Article CAS PubMed Google Scholar
• Blumenthal, T. Operons in eukaryotes. Brief. Funct. Genomic. Proteomic. 3, 199–211 (2004).
  Article CAS PubMed Google Scholar
• Ben-Shahar, Y., Nannapaneni, K., Casavant, T. L., Scheetz, T. E. & Welsh, M. J. Eukaryotic operon-like transcription of functionally related genes in Drosophila. Proc. Natl Acad. Sci. USA 104, 222–227 (2007).
  Article CAS PubMed Google Scholar
• Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969).
  Article CAS PubMed Google Scholar
• Waterston, R. H., Lander, E. S. & Sulston, J. E. On the sequencing of the human genome. Proc. Natl Acad. Sci. USA 99, 3712–3716 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Keene, J. D. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc. Natl Acad. Sci. USA 98, 7018–7024 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Keene, J. D. & Tenenbaum, S. A. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 9, 1161–1167 (2002).
  Article CAS PubMed Google Scholar
• Hieronymus, H. & Silver, P. A. A systems view of mRNP biology. Genes Dev. 18, 2845–2860 (2004). A comprehensive overview that articulates the advent of a new field in systems biology; the authors outline its conceptual framework and describe its experimental basis.
  Article CAS PubMed Google Scholar
• Moore, M. J. From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514–1518 (2005). A beautifully written essay that captivates the sequence of events by which eukaryotic mRNAs are transcribed, organized, processed and transported to reach their final fates of turnover and protein synthesis.
  Article CAS PubMed Google Scholar
• Keene, J. D. & Lager, P. J. Post-transcriptional operons and regulons co-ordinating gene expression. Chromosome Res. 13, 327–337 (2005).
  Article CAS PubMed Google Scholar
• Saunders, M. A., Liang, H. & Li, W. H. Human polymorphism at microRNAs and microRNA target sites. Proc. Natl Acad. Sci. USA 104, 3300–3305 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Chan, C. S., Elemento, O. & Tavazoie, S. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput. Biol. 1, e69 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Abdelmohsen, K. et al. Phosphorylation of HuR by Chk2 regulates SIRT1 expression. Mol. Cell 25, 543–557 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Intine, R. V., Tenenbaum, S. A., Sakulich, A. L., Keene, J. D. & Maraia, R. J. Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs. Mol. Cell 12, 1301–1307 (2003).
  Article CAS PubMed Google Scholar
• Garbarino-Pico, E. et al. Immediate early response of the circadian polyA ribonuclease nocturnin to two extracellular stimuli. RNA 13, 745–755 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).
  Article CAS PubMed Google Scholar
• Moore, M. J., Schwartzfarb, E. M., Silver, P. A. & Yu, M. C. Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. Mol. Cell 24, 903–915 (2006).
  Article CAS PubMed Google Scholar
• Sanford, J. R., Gray, N. K., Beckmann, K. & Caceres, J. F. A novel role for shuttling SR proteins in mRNA translation. Genes Dev. 18, 755–768 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Greenleaf, A. L. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18, 117–119 (1993).
  Article CAS PubMed Google Scholar
• Le Hir, H., Izaurralde, E., Maquat, L. E. & Moore, M. J. The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions. EMBO J. 19, 6860–6869 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Kaplan, J. C., Kahn, A. & Chelly, J. Illegitimate transcription: its use in the study of inherited disease. Hum. Mutat. 1, 357–360 (1992).
  Article CAS PubMed Google Scholar
• Blake, W. J., Kearn, M., Cantor, C. R. & Collins, J. J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003).
  Article CAS PubMed Google Scholar
• Rodriguez-Trelles, F., Tarrio, R. & Ayala, F. J. Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential? Bioessays 27, 592–601 (2005).
  Article CAS PubMed Google Scholar
• Yanai, I. et al. Similar gene expression profiles do not imply similar tissue functions. Trends Genet. 22, 132–138 (2006). A forward-thinking description of tissue-specific gene expression, its apparent leakiness and the suggestion that it involves coordinated post-transcriptional events.
  Article CAS PubMed Google Scholar
• Oliver, B., Parisi, M. & Clark, D. Gene expression neighborhoods. J. Biol. 1, 4 (2002).
  Article PubMed PubMed Central Google Scholar
• Aten, J. A. & Kanaar, R. Chromosomal organization: mingling with the neighbors. PLoS Biol. 4, e155 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Hurst, L. D., Pal, C. & Lercher, M. J. The evolutionary dynamics of eukaryotic gene order. Nature Rev. Genet. 5, 299–310 (2004).
  Article CAS PubMed Google Scholar
• Spellman, P. T. & Rubin, G. M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1, 5 (2002). A retrospective study of a large body of expression data from fruitflies, showing that co-localized genes are transcribed together in chromatin domains but the proteins that are encoded by these genes are not functionally related.
  Article PubMed PubMed Central Google Scholar
• Seydoux, G. & Braun, R. E. Pathway to totipotency: lessons from germ cells. Cell 127, 891–904 (2006). A review of current concepts in the field of germ-cell development that, among other things, suggests that totipotent germ cells use RNA-centric 'hubs' to provide plasticity in response to developmental signals.
  Article CAS PubMed Google Scholar
• Golding, I. & Cox, E. C. Eukaryotic transcription: what does it mean for a gene to be 'on'? Curr. Biol. 16, R371–R373 (2006).
  Article CAS PubMed Google Scholar
• Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Jin, L., Guzik, B. W., Bor, Y. C., Rekosh, D. & Hammarskjold, M. L. Tap and NXT promote translation of unspliced mRNA. Genes Dev. 17, 3075–3086 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Bor, Y. C. et al. The Wilms' tumor 1 (WT1) gene (+KTS isoform) functions with a CTE to enhance translation from an unspliced RNA with a retained intron. Genes Dev. 20, 1597–1608 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Gama-Carvalho, M., Barbosa-Morais, N. L., Brodsky, A. S., Silver, P. A. & Carmo-Fonseca, M. Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol. 7, R113 (2006). An elegant demonstration that the polypyrimidine tract RNA-binding protein and the U2AF2 splicing factors associate with discrete subsets of mature spliced mRNAs in the cytoplasm.
  Article CAS PubMed PubMed Central Google Scholar
• Keene, J. D. Why is Hu where? Shuttling of early-response-gene messenger RNA subsets. Proc. Natl Acad. Sci. USA 96, 5–7 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Zhu, H., Hasman, R. A., Barron, V. A., Luo, G. & Lou, H. A nuclear function of Hu proteins as neuron-specific alternative RNA processing regulators. Mol. Biol. Cell 17, 5105–5114 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212–1215 (2003).
  CAS PubMed Google Scholar
• Pan, Q. et al. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell 16, 929–941 (2004).
  Article CAS PubMed Google Scholar
• Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006).
  Article CAS PubMed Google Scholar
• Hieronymus, H. & Silver, P. A. Genome-wide analysis of RNA–protein interactions illustrates specificity of the mRNA export machinery. Nature Genet. 33, 155–161 (2003). A landmark paper describing how mRNA subsets that encode functionally related proteins associate combinatorially with export proteins Mex67 and Yra1 in yeast.
  Article CAS PubMed Google Scholar
• Guisbert, K., Duncan, K., Li, H. & Guthrie, C. Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. RNA 11, 383–393 (2005).
  Article CAS Google Scholar
• Tenenbaum, S. A., Carson, C. C., Lager, P. J. & Keene, J. D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl Acad. Sci. USA 97, 14085–14090 (2000). First use of RIP–chip to demonstrate that ELAV/Hu, EIF4E and PolyA-binding proteins associate with discrete mRNA subsets that changed coordinately following induction of neuronal differentiation.
  Article CAS PubMed PubMed Central Google Scholar
• Lai, W. S. et al. Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA. Mol. Cell. Biol. 19, 4311–4323 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Levine, T. D., Gao, F., King, P. H., Andrews, L. G. & Keene, J. D. Hel-N1: an autoimmune RNA-binding protein with specificity for 3′ uridylate-rich untranslated regions of growth factor mRNAs. Mol. Cell. Biol. 13, 3494–3504 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Brennan, C. M. & Steitz, J. A. HuR and mRNA stability. Cell Mol. Life Sci. 58, 266–277 (2001).
  Article CAS PubMed Google Scholar
• Antic, D. & Keene, J. D. Embryonic lethal abnormal visual RNA-binding proteins involved in growth, differentiation, and posttranscriptional gene expression. Am. J. Hum. Genet. 61, 273–278 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Cheadle, C. et al. Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability. BMC Genomics 6, 75 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lykke-Andersen, J. & Wagner, E. Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev. 19, 351–361 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lam, L. T. et al. Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. Genome Biol. 2, RESEARCH0041 (2001).
• Yang, E. et al. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res. 13, 1863–1872 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Raghavan, A. et al. Patterns of coordinate down-regulation of ARE-containing transcripts following immune cell activation. Genomics 84, 1002–1013 (2004).
  Article CAS PubMed Google Scholar
• Vlasova, I. A. et al. Coordinate stabilization of growth-regulatory transcripts in T cell malignancies. Genomics 86, 159–171 (2005). References 52–55 demonstrate that mRNA decay in immune cells can be classified into functional groups that change coordinately with cell activation or drug treatments.
  Article CAS PubMed Google Scholar
• Raghavan, A. et al. HuA and tristetraprolin are induced following T cell activation and display distinct but overlapping RNA binding specificities. J. Biol. Chem. 276, 47958–47965 (2001).
  Article CAS PubMed Google Scholar
• Marzluff, W. F. Metazoan replication-dependent histone mRNAs: a distinct set of RNA polymerase II transcripts. Curr. Opin. Cell Biol. 17, 274–280 (2005).
  Article CAS PubMed Google Scholar
• Townley-Tilson, W. H., Pendergrass, S. A., Marzluff, W. F. & Whitfield, M. L. Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein. RNA 12, 1853–1867 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, Y. et al. Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA 99, 5860–5865 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. D. & Hughes, T. R. Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol. Cell. Biol. 24, 5534–5547 (2004). References 59 and 60 demonstrate the existence of mRNA stability modules or post-transcriptional operons in yeast that can change coordinately following perturbations.
  Article CAS PubMed PubMed Central Google Scholar
• Duttagupta, R. et al. Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol. Cell. Biol. 25, 5499–5513 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lai, W. S., Carballo, E., Thorn, J. M., Kennington, E. A. & Blackshear, P. J. Interactions of CCCH zinc finger proteins with mRNA. Binding of tristetraprolin-related zinc finger proteins to AU-rich elements and destabilization of mRNA. J. Biol. Chem. 275, 17827–17837 (2000).
  Article CAS PubMed Google Scholar
• Puig, S., Askeland, E. & Thiele, D. J. Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell 120, 99–110 (2005).
  Article CAS PubMed Google Scholar
• Bell-Pedersen, D. et al. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nature Rev. Genet. 6, 544–556 (2005).
  Article CAS PubMed Google Scholar
• Benjamin, D., Schmidlin, M., Min, L., Gross, B. & Moroni, C. BRF1 protein turnover and mRNA decay activity are regulated by protein kinase B at the same phosphorylation sites. Mol. Cell. Biol. 26, 9497–9507 (2006). The authors note that BRF1 RNA-binding protein undergoes diurnal circadian pulses in peripheral organs, and might use phosphorylation to regulate a post-transcriptional operon that coordinates the degradation of immediate-early-gene transcripts.
  Article CAS PubMed PubMed Central Google Scholar
• Lowrey, P. L. & Takahashi, J. S. Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu. Rev. Genomics Hum. Genet. 5, 407–441 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Storch, K. F. et al. Extensive and divergent circadian gene expression in liver and heart. Nature 417, 78–83 (2002).
  Article CAS PubMed Google Scholar
• Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320 (2002).
  Article CAS PubMed Google Scholar
• Lidder, P., Gutierrez, R. A., Salome, P. A., McClung, C. R. & Green, P. J. Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. Plant Physiol. 138, 2374–2385 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Kojima, S. et al. LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc. Natl Acad. Sci. USA 104, 1859–1864 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Fan, J. et al. Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc. Natl Acad. Sci. USA 99, 10611–10616 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Fan, J. et al. En masse nascent transcription analysis to elucidate regulatory transcription factors. Nucleic Acids Res. 34, 1492–1500 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Tenenbaum, S. A., Carson, C. C., Atasoy, U. & Keene, J. D. Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317, 79–87 (2003).
  Article CAS PubMed Google Scholar
• Eberwine, J., Miyashiro, K., Kacharmina, J. E. & Job, C. Local translation of classes of mRNAs that are targeted to neuronal dendrites. Proc. Natl Acad. Sci. USA 98, 7080–7085 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, Y. S. & Richter, J. D. Regulation of local mRNA translation. Curr. Opin. Cell Biol. 16, 308–313 (2004).
  Article CAS PubMed Google Scholar
• Racki, W. J. & Richter, J. D. CPEB controls oocyte growth and follicle development in the mouse. Development 133, 4527–4537 (2006).
  Article CAS PubMed Google Scholar
• Richter, J. D. & Lorenz, L. J. Selective translation of mRNAs at synapses. Curr. Opin. Neurobiol. 12, 300–304 (2002).
  Article CAS PubMed Google Scholar
• Ashley, C. T. Jr, Wilkinson, K. D., Reines, D. & Warren, S. T. FMR1 protein: conserved RNP family domains and selective RNA binding. Science 262, 563–566 (1993).
  Article CAS PubMed Google Scholar
• Gao, F. B., Carson, C. C., Levine, T. & Keene, J. D. Selection of a subset of mRNAs from combinatorial 3′ untranslated region libraries using neuronal RNA-binding protein Hel-N1. Proc. Natl Acad. Sci. USA 91, 11207–11211 (1994). This paper describes multitargeting of subsets of mRNAs that contain a similar binding sequence for an ELAV/Hu RNA-binding protein and suggests that their expression is coordinated.
  Article CAS PubMed PubMed Central Google Scholar
• Jain, R. G., Andrews, L. G., McGowan, K. M., Pekala, P. H. & Keene, J. D. Ectopic expression of Hel-N1, an RNA-binding protein, increases glucose transporter (GLUT1) expression in 3T3-L1 adipocytes. Mol. Cell. Biol. 17, 954–962 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Brown, V. et al. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107, 477–487 (2001).
  Article CAS PubMed Google Scholar
• Eystathioy, T. et al. A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol. Biol. Cell 13, 1338–1351 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Waggoner, S. A. & Liebhaber, S. A. Identification of mRNAs associated with _α_CP2-containing RNP complexes. Mol. Cell. Biol. 23, 7055–7067 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Lopez de Silanes, I., Zhan, M., Lal, A., Yang, X. & Gorospe, M. Identification of a target RNA motif for RNA-binding protein HuR. Proc. Natl Acad. Sci. USA 101, 2987–2992 (2004).
  Article CAS PubMed Google Scholar
• Culjkovic, B., Topisirovic, I., Skrabanek, L., Ruiz-Gutierrez, M. & Borden, K. L. EIF4E is a central node of an RNA regulon that governs cellular proliferation. J. Cell. Biol. 175, 415–426 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Larsson, O. et al. Apoptosis resistance downstream of EIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure. Nucleic Acids Res. 34, 4375–4386 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Agnes, F. & Perron, M. RNA-binding proteins and neural development: a matter of targets and complexes. Neuroreport 15, 2567–2570 (2004).
  Article CAS PubMed Google Scholar
• Fan, J., Heller, N. M., Gorospe, M., Atasoy, U. & Stellato, C. The role of post-transcriptional regulation in chemokine gene expression in inflammation and allergy. Eur. Respir. J. 26, 933–947 (2005).
  Article CAS PubMed Google Scholar
• Mata, J., Marguerat, S. & Bahler, J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem. Sci. 30, 506–514 (2005).
  Article CAS PubMed Google Scholar
• Vanderklish, P. W. & Edelman, G. M. Differential translation and fragile X syndrome. Genes Brain Behav. 4, 360–384 (2005).
  Article CAS PubMed Google Scholar
• Vemuri, G. N. & Aristidou, A. A. Metabolic engineering in the omics era: elucidating and modulating regulatory networks. Microbiol. Mol. Biol. Rev. 69, 197–216 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Wilusz, C. J. & Wilusz, J. Bringing the role of mRNA decay in the control of gene expression into focus. Trends Genet. 20, 491–497 (2004).
  Article CAS PubMed Google Scholar
• Gerber, A. P., Herschlag, D. & Brown, P. O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2, E79 (2004). A definitive demonstration that five RNA-binding proteins in S. cerevisiae associate with discrete subsets of mRNAs that encode functionally related proteins. It provides a confirmation of modular RNPs that is consistent with the post-transcriptional operon model.
  Article PubMed PubMed Central Google Scholar
• Wickens, M., Bernstein, D. S., Kimble, J. & Parker, R. A PUF family portrait: 3′UTR regulation as a way of life. Trends Genet. 18, 150–157 (2002).
  Article CAS PubMed Google Scholar
• Garcia-Rodriguez, L. J., Gay, A. C. & Pon, L. A. Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast. J. Cell Biol. 176, 197–207 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Mesarovic, M. D., Sreenath, S. N. & Keene, J. D. Search for organising principles: understanding in systems biology. Syst. Biol. (Stevenage) 1, 19–27 (2004).
  Article CAS Google Scholar
• Gerber, A. P., Luschnig, S., Krasnow, M. A., Brown, P. O. & Herschlag, D. Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 103, 4487–4492 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Culjkovic, B., Topisirovic, I. & Borden, K. L. Controlling gene expression through RNA regulons: the role of the eukaryotic translation initiation factor EIF4E. Cell Cycle 6, 65–69 (2007).
  Article CAS PubMed Google Scholar
• Mamane, Y. et al. Epigenetic activation of a subset of mRNAs by EIF4E explains its effects on cell proliferation. PLoS ONE 2, e242 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Lu, X., de la Pena, L., Barker, C., Camphausen, K. & Tofilon, P. J. Radiation-induced changes in gene expression involve recruitment of existing messenger RNAs to and away from polysomes. Cancer Res. 66, 1052–161 (2006).
  Article PubMed Google Scholar
• Mazan-Mamczarz, K. et al. RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. Proc. Natl Acad. Sci. USA 100, 8354–8359 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Gorospe, M. HuR in the mammalian genotoxic response: post-transcriptional multitasking. Cell Cycle 2, 412–414 (2003).
  Article CAS PubMed Google Scholar
• Lopez de Silanes, I. et al. Global analysis of HuR-regulated gene expression in colon cancer systems of reducing complexity. Gene Expr. 12, 49–59 (2004).
  Article CAS PubMed Google Scholar
• Lopez de Silanes, I. et al. Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1. Mol. Cell. Biol. 25, 9520–9531 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Penalva, L. O., Burdick, M. D., Lin, S. M., Sutterluety, H. & Keene, J. D. RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells. Mol. Cancer 3, 24 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Kedersha, N. et al. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 169, 871–884 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Casciola-Rosen, L., Rosen, A., Petri, M. & Schlissel, M. Surface blebs on apoptotic cells are sites of enhanced procoagulant activity: implications for coagulation events and antigenic spread in systemic lupus erythematosus. Proc. Natl Acad. Sci. USA 93, 1624–1629 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Gould, S. J., Booth, A. M. & Hildreth, J. E. The Trojan exosome hypothesis. Proc. Natl Acad. Sci. USA 100, 10592–10597 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Valadi, H. et al. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nature Cell Biol. 7 May 2007 (doi: 10.1038/ncb1596).
  Article CAS PubMed Google Scholar
• Lawrence, J. G. Selfish operons and speciation by gene transfer. Trends Microbiol. 5, 355–359 (1997).
  Article CAS PubMed Google Scholar
• Lawrence, J. G. Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 110, 407–413 (2002).
  Article CAS PubMed Google Scholar
• Carballo, E., Lai, W. S. & Blackshear, P. J. Evidence that tristetraprolin is a physiological regulator of granulocyte–macrophage colony-stimulating factor messenger RNA deadenylation and stability. Blood 95, 1891–1899 (2000).
  CAS PubMed Google Scholar
• Musunuru, K. Cell-specific RNA-binding proteins in human disease. Trends Cardiovasc. Med. 13, 188–195 (2003).
  Article CAS PubMed Google Scholar
• Ruggero, D. et al. Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification. Science 299, 259–262 (2003).
  Article CAS PubMed Google Scholar
• Verheesen, P. et al. Prevention of oculopharyngeal muscular dystrophy-associated aggregation of nuclear polyA-binding protein with a single-domain intracellular antibody. Hum. Mol. Genet. 15, 105–111 (2006).
  Article CAS PubMed Google Scholar
• Parsa, A. T. & Holland, E. C. Cooperative translational control of gene expression by Ras and Akt in cancer. Trends Mol. Med. 10, 607–613 (2004).
  Article CAS PubMed Google Scholar
• Polunovsky, V. A. & Bitterman, P. B. The cap-dependent translation apparatus integrates and amplifies cancer pathways. RNA Biol. 3, 10–17 (2006).
  Article CAS PubMed Google Scholar
• Taylor, G. A. et al. A pathogenetic role for TNFa in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency. Immunity 4, 445–454 (1996).
  Article CAS PubMed Google Scholar
• van der Walt, J. M. et al. Fibroblast growth factor 20 polymorphisms and haplotypes strongly influence risk of Parkinson disease. Am. J. Hum. Genet. 74, 1121–1127 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Hollams, E. M., Giles, K. M., Thomson, A. M. & Leedman, P. J. mRNA stability and the control of gene expression: implications for human disease. Neurochem. Res. 27, 957–980 (2002).
  Article CAS PubMed Google Scholar
• Audic, Y. & Hartley, R. S. Post-transcriptional regulation in cancer. Biol. Cell 96, 479–498 (2004).
  Article CAS PubMed Google Scholar
• Niehrs, C. & Pollet, N. Synexpression groups in eukaryotes. Nature 402, 483–487 (1999).
  Article CAS PubMed Google Scholar
• Inada, M. & Guthrie, C. 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).
  Article CAS PubMed PubMed Central Google Scholar
• Darnell, R. B. & Posner, J. B. Paraneoplastic syndromes affecting the nervous system. Semin. Oncol. 33, 270–298 (2006).
  Article PubMed Google Scholar
• Lasker, A. G., Mazzocco, M. M. & Zee, D. S. Ocular motor indicators of executive dysfunction in fragile X and Turner syndromes. Brain. Cogn. 63, 203–220 (2006).
  Article PubMed Google Scholar
• Wong, J. M. & Collins, K. Telomerase RNA level limits telomere maintenance in X-linked dyskeratosis congenita. Genes Dev. 20, 2848–2858 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Robinson, D. O., Hammans, S. R., Read, S. P. & Sillibourne, J. Oculopharyngeal muscular dystrophy (OPMD): analysis of the PABPN1 gene expansion sequence in 86 patients reveals 13 different expansion types and further evidence for unequal recombination as the mutational mechanism. Hum. Genet. 116, 267–271 (2005).
  Article CAS PubMed Google Scholar
• Carrel, T. L. et al. Survival motor neuron function in motor axons is independent of functions required for small nuclear ribonucleoprotein biogenesis. J. Neurosci. 26, 11014–11022 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ranum, L. P. & Cooper, T. A. RNA-mediated neuromuscular disorders. Annu. Rev. Neurosci. 29, 259–277 (2006).
  Article CAS PubMed Google Scholar
• Shiffman, D. et al. Gene variants of VAMP8 and HNRPUL1 are associated with early-onset myocardial infarction. Arterioscler. Thromb. Vasc. Biol. 26, 1613–1618 (2006).
  Article CAS PubMed Google Scholar
• Artandi, S. E. Telomeres, telomerase, and human disease. N. Engl. J. Med. 355, 1195–1197 (2006).
  Article CAS PubMed Google Scholar
• Siddall, N. A., McLaughlin, E. A., Marriner, N. L. & Hime, G. R. The RNA-binding protein Musashi is required intrinsically to maintain stem cell identity. Proc. Natl Acad. Sci. USA 103, 8402–8407 (2006).
  Article CAS PubMed PubMed Central Google Scholar