3'-UTR-located inverted Alu repeats facilitate mRNA translational repression and stress granule accumulation

References

• Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al, International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409:860 - 921; http://dx.doi.org/10.1038/35057062; PMID: 11237011
   PubMed Web of Science ®Google Scholar
• Yulug IG, Yulug A, Fisher EM. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics 1995; 27:544 - 8; http://dx.doi.org/10.1006/geno.1995.1090; PMID: 7558040
   PubMed Web of Science ®Google Scholar
• Mignone F, Gissi C, Liuni S, Pesole G.. Untranslated regions of mRNAs. Genome Biol 2002; 3:REVIEWS0004
   PubMed Web of Science ®Google Scholar
• Mazumder B, Seshadri V, Fox PL. Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 2003; 28:91 - 8; http://dx.doi.org/10.1016/S0968-0004(03)00002-1; PMID: 12575997
   PubMed Web of Science ®Google Scholar
• Andreassi C, Riccio A. To localize or not to localize: mRNA fate is in 3’UTR ends. Trends Cell Biol 2009; 19:465 - 74; http://dx.doi.org/10.1016/j.tcb.2009.06.001; PMID: 19716303
   PubMed Web of Science ®Google Scholar
• Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell 2009; 136:719 - 30; http://dx.doi.org/10.1016/j.cell.2009.01.044; PMID: 19239891
   PubMed Web of Science ®Google Scholar
• An HJ, Lee D, Lee KH, Bhak J. The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3′ untranslated regions. BMC Genomics 2004; 5:97; http://dx.doi.org/10.1186/1471-2164-5-97; PMID: 15610565
   PubMed Web of Science ®Google Scholar
• Chakkalakal JV, Miura P, Bélanger G, Michel RN, Jasmin BJ. Modulation of utrophin A mRNA stability in fast versus slow muscles via an AU-rich element and calcineurin signaling. Nucleic Acids Res 2008; 36:826 - 38; http://dx.doi.org/10.1093/nar/gkm1107; PMID: 18084024
   PubMed Web of Science ®Google Scholar
• Xin H, Brown JA, Gong C, Fan H, Brewer G, Gnarra JR. Association of the von Hippel-Lindau protein with AUF1 and post-transcriptional regulation of Vascular Endothelial Growth Factor A mRNA. Mol Cancer Res 2011; PMID: 22086907
   PubMed Web of Science ®Google Scholar
• McGray AJ, Gingerich T, Petrik JJ, Lamarre J. Regulation of thrombospondin-1 expression through AU-rich elements in the 3’UTR of the mRNA. Cell Mol Biol Lett 2011; 16:55 - 68; http://dx.doi.org/10.2478/s11658-010-0037-x; PMID: 21161418
   PubMed Web of Science ®Google Scholar
• Smalheiser NR, Torvik VI. Alu elements within human mRNAs are probable microRNA targets. Trends Genet 2006; 22:532 - 6; http://dx.doi.org/10.1016/j.tig.2006.08.007; PMID: 16914224
   PubMed Web of Science ®Google Scholar
• Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 2011; 470:284 - 8; http://dx.doi.org/10.1038/nature09701; PMID: 21307942
   PubMed Web of Science ®Google Scholar
• Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, et al. Regulating gene expression through RNA nuclear retention. Cell 2005; 123:249 - 63; http://dx.doi.org/10.1016/j.cell.2005.08.033; PMID: 16239143
   PubMed Web of Science ®Google Scholar
• Hogg M, Paro S, Keegan LP, O’Connell MA. RNA editing by mammalian ADARs. Adv Genet 2011; 73:87 - 120; http://dx.doi.org/10.1016/B978-0-12-380860-8.00003-3; PMID: 21310295
   PubMed Web of Science ®Google Scholar
• Chen LL, DeCerbo JN, Carmichael GG. Alu element-mediated gene silencing. EMBO J 2008; 27:1694 - 705; http://dx.doi.org/10.1038/emboj.2008.94; PMID: 18497743
   PubMed Web of Science ®Google Scholar
• Kingston RE, Chen CA, Okayama H. Calcium phosphate transfection. Curr Protoc Immunol 2001; Chapter 10:Unit 10 3.
   Google Scholar
• Khabar KS. The AU-rich transcriptome: more than interferons and cytokines, and its role in disease. J Interferon Cytokine Res 2005; 25:1 - 10; http://dx.doi.org/10.1089/jir.2005.25.1; PMID: 15684617
   PubMed Web of Science ®Google Scholar
• Khabar KS, Bakheet T, Williams BR. AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach. Genomics 2005; 85:165 - 75; http://dx.doi.org/10.1016/j.ygeno.2004.10.004; PMID: 15676275
   PubMed Web of Science ®Google Scholar
• Mazumder B, Seshadri V, Imataka H, Sonenberg N, Fox PL. Translational silencing of ceruloplasmin requires the essential elements of mRNA circularization: poly(A) tail, poly(A)-binding protein, and eukaryotic translation initiation factor 4G. Mol Cell Biol 2001; 21:6440 - 9; http://dx.doi.org/10.1128/MCB.21.19.6440-6449.2001; PMID: 11533233
   PubMed Web of Science ®Google Scholar
• Chartrand P, Meng XH, Singer RH, Long RM. Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo. Curr Biol 1999; 9:333 - 6; http://dx.doi.org/10.1016/S0960-9822(99)80144-4; PMID: 10209102
   PubMed Web of Science ®Google Scholar
• Casey JL, Hentze MW, Koeller DM, Caughman SW, Rouault TA, Klausner RD, et al. Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation. Science 1988; 240:924 - 8; http://dx.doi.org/10.1126/science.2452485; PMID: 2452485
   PubMed Web of Science ®Google Scholar
• Tanguay RL, Gallie DR. Translational efficiency is regulated by the length of the 3′ untranslated region. Mol Cell Biol 1996; 16:146 - 56; PMID: 8524291
   PubMed Web of Science ®Google Scholar
• Balmer LA, Beveridge DJ, Jazayeri JA, Thomson AM, Walker CE, Leedman PJ. Identification of a novel AU-Rich element in the 3′ untranslated region of epidermal growth factor receptor mRNA that is the target for regulated RNA-binding proteins. Mol Cell Biol 2001; 21:2070 - 84; http://dx.doi.org/10.1128/MCB.21.6.2070-2084.2001; PMID: 11238942
   PubMed Web of Science ®Google Scholar
• Yang Q, McDermott PJ, Duzic E, Pleij CW, Sherlock JD, Lanier SM. The 3′-untranslated region of the alpha2C-adrenergic receptor mRNA impedes translation of the receptor message. J Biol Chem 1997; 272:15466 - 73; http://dx.doi.org/10.1074/jbc.272.24.15466; PMID: 9182579
   PubMed Web of Science ®Google Scholar
• Mazroui R, Huot ME, Tremblay S, Filion C, Labelle Y, Khandjian EW. Trapping of messenger RNA by Fragile X Mental Retardation protein into cytoplasmic granules induces translation repression. Hum Mol Genet 2002; 11:3007 - 17; http://dx.doi.org/10.1093/hmg/11.24.3007; PMID: 12417522
   PubMed Web of Science ®Google Scholar
• Krichevsky AM, Kosik KS. Neuronal RNA granules: a link between RNA localization and stimulation-dependent translation. Neuron 2001; 32:683 - 96; http://dx.doi.org/10.1016/S0896-6273(01)00508-6; PMID: 11719208
   PubMed Web of Science ®Google Scholar
• Hu S, Claud EC, Musch MW, Chang EB. Stress granule formation mediates the inhibition of colonic Hsp70 translation by interferon-gamma and tumor necrosis factor-alpha. Am J Physiol Gastrointest Liver Physiol 2010; 298:G481 - 92; http://dx.doi.org/10.1152/ajpgi.00234.2009; PMID: 20110459
   PubMed Web of Science ®Google Scholar
• Carbonaro M, O’Brate A, Giannakakou P. Microtubule disruption targets HIF-1alpha mRNA to cytoplasmic P-bodies for translational repression. J Cell Biol 2011; 192:83 - 99; http://dx.doi.org/10.1083/jcb.201004145; PMID: 21220510
   PubMed Web of Science ®Google Scholar
• Bass BL. RNA editing and hypermutation by adenosine deamination. Trends Biochem Sci 1997; 22:157 - 62; http://dx.doi.org/10.1016/S0968-0004(97)01035-9; PMID: 9175473
   PubMed Web of Science ®Google Scholar
• Lehmann KA, Bass BL. The importance of internal loops within RNA substrates of ADAR1. J Mol Biol 1999; 291:1 - 13; http://dx.doi.org/10.1006/jmbi.1999.2914; PMID: 10438602
   PubMed Web of Science ®Google Scholar
• Borchert GM, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, et al. Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum Mol Genet 2009; 18:4801 - 7; http://dx.doi.org/10.1093/hmg/ddp443; PMID: 19776031
   PubMed Web of Science ®Google Scholar
• Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G. RNA-editing-mediated exon evolution. Genome Biol 2007; 8:R29; http://dx.doi.org/10.1186/gb-2007-8-2-r29; PMID: 17326827
   PubMed Web of Science ®Google Scholar
• Anderson P, Kedersha N. RNA granules. J Cell Biol 2006; 172:803 - 8; http://dx.doi.org/10.1083/jcb.200512082; PMID: 16520386
   PubMed Web of Science ®Google Scholar
• Kimball SR, Horetsky RL, Ron D, Jefferson LS, Harding HP. Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes. Am J Physiol Cell Physiol 2003; 284:C273 - 84; PMID: 12388085
   PubMed Web of Science ®Google Scholar
• Mollet S, Cougot N, Wilczynska A, Dautry F, Kress M, Bertrand E, et al. Translationally repressed mRNA transiently cycles through stress granules during stress. Mol Biol Cell 2008; 19:4469 - 79; http://dx.doi.org/10.1091/mbc.E08-05-0499; PMID: 18632980
   PubMed Web of Science ®Google Scholar
• Stoecklin G, Stubbs T, Kedersha N, Wax S, Rigby WF, Blackwell TK, et al. MK2-induced tristetraprolin:14-3-3 complexes prevent stress granule association and ARE-mRNA decay. EMBO J 2004; 23:1313 - 24; http://dx.doi.org/10.1038/sj.emboj.7600163; PMID: 15014438
   PubMed Web of Science ®Google Scholar
• Kedersha N, Anderson P. Stress granules: sites of mRNA triage that regulate mRNA stability and translatability. Biochem Soc Trans 2002; 30:963 - 9; http://dx.doi.org/10.1042/BST0300963; PMID: 12440955
   PubMed Web of Science ®Google Scholar
• Wilczynska A, Aigueperse C, Kress M, Dautry F, Weil D. The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules. J Cell Sci 2005; 118:981 - 92; http://dx.doi.org/10.1242/jcs.01692; PMID: 15731006
   PubMed Web of Science ®Google Scholar
• Yang WH, Yu JH, Gulick T, Bloch KD, Bloch DB. RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules. RNA 2006; 12:547 - 54; http://dx.doi.org/10.1261/rna.2302706; PMID: 16484376
   PubMed Web of Science ®Google Scholar
• Yang WH, Bloch DB. Probing the mRNA processing body using protein macroarrays and “autoantigenomics”. RNA 2007; 13:704 - 12; http://dx.doi.org/10.1261/rna.411907; PMID: 17339575
   PubMed Web of Science ®Google Scholar
• Kedersha NL, Gupta M, Li W, Miller I, Anderson P. RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules. J Cell Biol 1999; 147:1431 - 42; http://dx.doi.org/10.1083/jcb.147.7.1431; PMID: 10613902
   PubMed Web of Science ®Google Scholar
• Scadden AD. Inosine-containing dsRNA binds a stress-granule-like complex and downregulates gene expression in trans. Mol Cell 2007; 28:491 - 500; http://dx.doi.org/10.1016/j.molcel.2007.09.005; PMID: 17996712
   PubMed Web of Science ®Google Scholar
• Pare JM, Lopez-Orozco J, Hobman TC. Live cell imaging of Argonaute proteins in mammalian cells. Methods Mol Biol 2011; 725:161 - 72; http://dx.doi.org/10.1007/978-1-61779-046-1_11; PMID: 21528453
   PubMedGoogle Scholar
• Chaumeil J, Augui S, Chow JC, Heard E. Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation. Methods Mol Biol 2008; 463:297 - 308; http://dx.doi.org/10.1007/978-1-59745-406-3_18; PMID: 18951174
   PubMedGoogle Scholar