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Review

Nuclear function of Alus

&
Pages 131-137 | Received 05 Nov 2013, Accepted 27 Jan 2014, Published online: 04 Feb 2014

References

  • Rebollo R, Horard B, Hubert B, Vieira C. Jumping genes and epigenetics: Towards new species. Gene 2010; 454:1 - 7; http://dx.doi.org/10.1016/j.gene.2010.01.003; PMID: 20102733
  • Cordaux R, Hedges DJ, Herke SW, Batzer MA. Estimating the retrotransposition rate of human Alu elements. Gene 2006; 373:134 - 7; http://dx.doi.org/10.1016/j.gene.2006.01.019; PMID: 16522357
  • Kazazian HH Jr.. An estimated frequency of endogenous insertional mutations in humans. Nat Genet 1999; 22:130; http://dx.doi.org/10.1038/9638; PMID: 10369250
  • Li X, Scaringe WA, Hill KA, Roberts S, Mengos A, Careri D, Pinto MT, Kasper CK, Sommer SS. Frequency of recent retrotransposition events in the human factor IX gene. Hum Mutat 2001; 17:511 - 9; http://dx.doi.org/10.1002/humu.1134; PMID: 11385709
  • McCLINTOCK B. Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 1951; 16:13 - 47; http://dx.doi.org/10.1101/SQB.1951.016.01.004; PMID: 14942727
  • Batzer MA, Schmid CW, Deininger PL. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol 1993; 224:213 - 32; http://dx.doi.org/10.1016/0076-6879(93)24017-O; PMID: 8264388
  • Ponicsan SL, Kugel JF, Goodrich JA. Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev 2010; 20:149 - 55; http://dx.doi.org/10.1016/j.gde.2010.01.004; PMID: 20176473
  • Schmitz J. SINEs as driving forces in genome evolution. Genome Dyn 2012; 7:92 - 107; http://dx.doi.org/10.1159/000337117; PMID: 22759815
  • Rubin CM, Houck CM, Deininger PL, Friedmann T, Schmid CW. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature 1980; 284:372 - 4; http://dx.doi.org/10.1038/284372a0; PMID: 6244506
  • Jelinek WR, Toomey TP, Leinwand L, Duncan CH, Biro PA, Choudary PV, Weissman SM, Rubin CM, Houck CM, Deininger PL, et al. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A 1980; 77:1398 - 402; http://dx.doi.org/10.1073/pnas.77.3.1398; PMID: 6246492
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, 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
  • Houck CM, Rinehart FP, Schmid CW. A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 1979; 132:289 - 306; http://dx.doi.org/10.1016/0022-2836(79)90261-4; PMID: 533893
  • Batzer MA, Schmid CW, Deininger PL. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol 1993; 224:213 - 32; http://dx.doi.org/10.1016/0076-6879(93)24017-O; PMID: 8264388
  • Ullu E, Tschudi C. Alu sequences are processed 7SL RNA genes. Nature 1984; 312:171 - 2; http://dx.doi.org/10.1038/312171a0; PMID: 6209580
  • Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002; 3:370 - 9; http://dx.doi.org/10.1038/nrg798; PMID: 11988762
  • Hancks DC, Kazazian HH Jr.. Active human retrotransposons: variation and disease. Curr Opin Genet Dev 2012; 22:191 - 203; http://dx.doi.org/10.1016/j.gde.2012.02.006; PMID: 22406018
  • Deininger P. Alu elements: know the SINEs. Genome Biol 2011; 12:236; http://dx.doi.org/10.1186/gb-2011-12-12-236; PMID: 22204421
  • Deininger PL, Batzer MA. Alu repeats and human disease. Mol Genet Metab 1999; 67:183 - 93; http://dx.doi.org/10.1006/mgme.1999.2864; PMID: 10381326
  • Oler AJ, Traina-Dorge S, Derbes RS, Canella D, Cairns BR, Roy-Engel AM. Alu expression in human cell lines and their retrotranspositional potential. Mob DNA 2012; 3:11; http://dx.doi.org/10.1186/1759-8753-3-11; PMID: 22716230
  • Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res 2008; 18:1875 - 83; http://dx.doi.org/10.1101/gr.081737.108; PMID: 18836035
  • Rebollo R, Romanish MT, Mager DL. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 2012; 46:21 - 42; http://dx.doi.org/10.1146/annurev-genet-110711-155621; PMID: 22905872
  • Huda A, Mariño-Ramírez L, Jordan IK. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA 2010; 1:2; http://dx.doi.org/10.1186/1759-8753-1-2; PMID: 20226072
  • Canella D, Praz V, Reina JH, Cousin P, Hernandez N. Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 2010; 20:710 - 21; http://dx.doi.org/10.1101/gr.101337.109; PMID: 20413673
  • Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 2010; 17:635 - 40; http://dx.doi.org/10.1038/nsmb.1794; PMID: 20418883
  • Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, et al. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol 2010; 17:620 - 8; http://dx.doi.org/10.1038/nsmb.1801; PMID: 20418882
  • Goodier JL, Cheung LE, Kazazian HH Jr.. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet 2012; 8:e1002941; http://dx.doi.org/10.1371/journal.pgen.1002941; PMID: 23093941
  • Britten RJ. Transposable element insertions have strongly affected human evolution. Proc Natl Acad Sci U S A 2010; 107:19945 - 8; http://dx.doi.org/10.1073/pnas.1014330107; PMID: 21041622
  • Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 2010; 141:1253 - 61; http://dx.doi.org/10.1016/j.cell.2010.05.020; PMID: 20603005
  • Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, et al. Mobile interspersed repeats are major structural variants in the human genome. Cell 2010; 141:1171 - 82; http://dx.doi.org/10.1016/j.cell.2010.05.026; PMID: 20602999
  • Valente L, Nishikura K. ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog Nucleic Acid Res Mol Biol 2005; 79:299 - 338; http://dx.doi.org/10.1016/S0079-6603(04)79006-6; PMID: 16096031
  • Jepson JEC, Reenan RA. Adenosine-to-inosine genetic recoding is required in the adult stage nervous system for coordinated behavior in Drosophila. J Biol Chem 2009; 284:31391 - 400; http://dx.doi.org/10.1074/jbc.M109.035048; PMID: 19759011
  • Mattick JS, Mehler MF. RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci 2008; 31:227 - 33; http://dx.doi.org/10.1016/j.tins.2008.02.003; PMID: 18395806
  • Wimmer K, Callens T, Wernstedt A, Messiaen L. The NF1 gene contains hotspots for L1 endonuclease-dependent de novo insertion. PLoS Genet 2011; 7:e1002371; http://dx.doi.org/10.1371/journal.pgen.1002371; PMID: 22125493
  • Chae JJ, Park YB, Kim SH, Hong SS, Song GJ, Han KH, Namkoong Y, Kim HS, Lee CC. Two partial deletion mutations involving the same Alu sequence within intron 8 of the LDL receptor gene in Korean patients with familial hypercholesterolemia. Hum Genet 1997; 99:155 - 63; http://dx.doi.org/10.1007/s004390050331; PMID: 9048913
  • Lehrman MA, Goldstein JL, Russell DW, Brown MS. Duplication of seven exons in LDL receptor gene caused by Alu-Alu recombination in a subject with familial hypercholesterolemia. Cell 1987; 48:827 - 35; http://dx.doi.org/10.1016/0092-8674(87)90079-1; PMID: 3815525
  • Lehrman MA, Schneider WJ, Südhof TC, Brown MS, Goldstein JL, Russell DW. Mutation in LDL receptor: Alu-Alu recombination deletes exons encoding transmembrane and cytoplasmic domains. Science 1985; 227:140 - 6; http://dx.doi.org/10.1126/science.3155573; PMID: 3155573
  • Rüdiger NS, Heinsvig EM, Hansen FA, Faergeman O, Bolund L, Gregersen N. DNA deletions in the low density lipoprotein (LDL) receptor gene in Danish families with familial hypercholesterolemia. Clin Genet 1991; 39:451 - 62; http://dx.doi.org/10.1111/j.1399-0004.1991.tb03057.x; PMID: 1863993
  • Yamakawa K, Takada K, Yanagi H, Tsuchiya S, Kawai K, Nakagawa S, Kajiyama G, Hamaguchi H. Three novel partial deletions of the low-density lipoprotein (LDL) receptor gene in familial hypercholesterolemia. Hum Genet 1989; 82:317 - 21; http://dx.doi.org/10.1007/BF00273989; PMID: 2544509
  • Puget N, Sinilnikova OM, Stoppa-Lyonnet D, Audoynaud C, Pagès S, Lynch HT, Goldgar D, Lenoir GM, Mazoyer S. An Alu-mediated 6-kb duplication in the BRCA1 gene: a new founder mutation?. Am J Hum Genet 1999; 64:300 - 2; http://dx.doi.org/10.1086/302211; PMID: 9915971
  • Swensen J, Hoffman M, Skolnick MH, Neuhausen SL. Identification of a 14 kb deletion involving the promoter region of BRCA1 in a breast cancer family. Hum Mol Genet 1997; 6:1513 - 7; http://dx.doi.org/10.1093/hmg/6.9.1513; PMID: 9285788
  • Miki Y, Katagiri T, Kasumi F, Yoshimoto T, Nakamura Y. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet 1996; 13:245 - 7; http://dx.doi.org/10.1038/ng0696-245; PMID: 8640237
  • Teugels E, De Brakeleer S, Goelen G, Lissens W, Sermijn E, De Grève J. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mutat 2005; 26:284 - 284; http://dx.doi.org/10.1002/humu.9366; PMID: 16088935
  • McClintock B. The significance of responses of the genome to challenge. Science 1984; 226:792 - 801; http://dx.doi.org/10.1126/science.15739260; PMID: 15739260
  • Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, et al. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 2009; 41:563 - 71; http://dx.doi.org/10.1038/ng.368; PMID: 19377475
  • Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 2007; 41:331 - 68; http://dx.doi.org/10.1146/annurev.genet.40.110405.090448; PMID: 18076328
  • Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006; 441:87 - 90; http://dx.doi.org/10.1038/nature04696; PMID: 16625209
  • Polak P, Domany E. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 2006; 7:133; http://dx.doi.org/10.1186/1471-2164-7-133; PMID: 16740159
  • Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, et al. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet 2013; 9:e1003588; http://dx.doi.org/10.1371/journal.pgen.1003588; PMID: 23861667
  • Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M. CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol 2011; 3:1304 - 11; http://dx.doi.org/10.1093/gbe/evr107; PMID: 22016335
  • Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M. Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 2009; 25:63 - 6; http://dx.doi.org/10.1016/j.tig.2008.11.005; PMID: 19101055
  • Cui F, Sirotin MV, Zhurkin VB. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct 2011; 6:2; http://dx.doi.org/10.1186/1745-6150-6-2; PMID: 21208455
  • Witherspoon DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, Hedges DJ, Batzer MA, Jorde LB. Alu repeats increase local recombination rates. BMC Genomics 2009; 10:530; http://dx.doi.org/10.1186/1471-2164-10-530; PMID: 19917129
  • Waldman AS, Liskay RM. Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology. Mol Cell Biol 1988; 8:5350 - 7; PMID: 2854196
  • Pangrazio A, Caldana ME, Sobacchi C, Panaroni C, Susani L, Mihci E, Cavaliere ML, Giliani S, Villa A, Frattini A. Characterization of a novel Alu-Alu recombination-mediated genomic deletion in the TCIRG1 gene in five osteopetrotic patients. J Bone Miner Res 2009; 24:162 - 7; http://dx.doi.org/10.1359/jbmr.080818; PMID: 18715141
  • Purandare SM, Patel PI. Recombination hot spots and human disease. Genome Res 1997; 7:773 - 86; PMID: 9267802
  • Lehrman MA, Goldstein JL, Russell DW, Brown MS. Duplication of seven exons in LDL receptor gene caused by Alu-Alu recombination in a subject with familial hypercholesterolemia. Cell 1987; 48:827 - 35; http://dx.doi.org/10.1016/0092-8674(87)90079-1; PMID: 3815525
  • Nyström-Lahti M, Kristo P, Nicolaides NC, Chang S-Y, Aaltonen LA, Moisio A-L, Järvinen HJ, Mecklin J-P, Kinzler KW, Vogelstein B, et al. Founding mutations and Alu-mediated recombination in hereditary colon cancer. Nat Med 1995; 1:1203 - 6; http://dx.doi.org/10.1038/nm1195-1203; PMID: 7584997
  • Franke G, Bausch B, Hoffmann MM, Cybulla M, Wilhelm C, Kohlhase J, Scherer G, Neumann HPH. Alu-Alu recombination underlies the vast majority of large VHL germline deletions: Molecular characterization and genotype-phenotype correlations in VHL patients. Hum Mutat 2009; 30:776 - 86; http://dx.doi.org/10.1002/humu.20948; PMID: 19280651
  • Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?. Genome Res 2012; 22:993 - 1005; http://dx.doi.org/10.1101/gr.134395.111; PMID: 22456607
  • Durkin SG, Glover TW. Chromosome fragile sites. Annu Rev Genet 2007; 41:169 - 92; http://dx.doi.org/10.1146/annurev.genet.41.042007.165900; PMID: 17608616
  • Glover TW, Stein CK. Induction of sister chromatid exchanges at common fragile sites. Am J Hum Genet 1987; 41:882 - 90; PMID: 3674017
  • Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, et al. Identification of early replicating fragile sites that contribute to genome instability. Cell 2013; 152:620 - 32; http://dx.doi.org/10.1016/j.cell.2013.01.006; PMID: 23352430
  • Hancks DC, Kazazian HH Jr.. Active human retrotransposons: variation and disease. Curr Opin Genet Dev 2012; 22:191 - 203; http://dx.doi.org/10.1016/j.gde.2012.02.006; PMID: 22406018
  • Häsler J, Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res 2006; 34:5491 - 7; http://dx.doi.org/10.1093/nar/gkl706; PMID: 17020921
  • Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res 2002; 12:1060 - 7; http://dx.doi.org/10.1101/gr.229302; PMID: 12097342
  • Zhang XH, Chasin LA. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci U S A 2006; 103:13427 - 32; http://dx.doi.org/10.1073/pnas.0603042103; PMID: 16938881
  • Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 2013; 152:453 - 66; http://dx.doi.org/10.1016/j.cell.2012.12.023; PMID: 23374342
  • Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 2003; 300:1288 - 91; http://dx.doi.org/10.1126/science.1082588; PMID: 12764196
  • Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, Graur D, Ast G. Minimal conditions for exonization of intronic sequences: 5′ splice site formation in alu exons. Mol Cell 2004; 14:221 - 31; http://dx.doi.org/10.1016/S1097-2765(04)00181-9; PMID: 15099521
  • Singer SS, Männel DN, Hehlgans T, Brosius J, Schmitz J. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. J Mol Biol 2004; 341:883 - 6; http://dx.doi.org/10.1016/j.jmb.2004.06.070; PMID: 15328599
  • Häsler J, Samuelsson T, Strub K. Useful ‘junk’: Alu RNAs in the human transcriptome. Cell Mol Life Sci 2007; 64:1793 - 800; http://dx.doi.org/10.1007/s00018-007-7084-0; PMID: 17514354
  • 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
  • Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2010; 127:135 - 54; http://dx.doi.org/10.1007/s00439-009-0752-4; PMID: 19823873
  • Sorek R. The birth of new exons: mechanisms and evolutionary consequences. RNA 2007; 13:1603 - 8; http://dx.doi.org/10.1261/rna.682507; PMID: 17709368
  • Warf MB, Diegel JV, von Hippel PH, Berglund JA. The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing. Proc Natl Acad Sci U S A 2009; 106:9203 - 8; http://dx.doi.org/10.1073/pnas.0900342106; PMID: 19470458
  • Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet 2008; 4:e1000225; http://dx.doi.org/10.1371/journal.pgen.1000225; PMID: 18841251
  • 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
  • Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ, Spector DL. 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
  • Chen L-L, Carmichael GG. Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle 2008; 7:3294 - 301; http://dx.doi.org/10.4161/cc.7.21.6927; PMID: 18948735
  • Capshew CR, Dusenbury KL, Hundley HA. Inverted Alu dsRNA structures do not affect localization but can alter translation efficiency of human mRNAs independent of RNA editing. Nucleic Acids Res 2012; 40:8637 - 45; http://dx.doi.org/10.1093/nar/gks590; PMID: 22735697
  • Fitzpatrick T, Huang S. 3′-UTR-located inverted Alu repeats facilitate mRNA translational repression and stress granule accumulation. Nucleus 2012; 3:359 - 69; http://dx.doi.org/10.4161/nucl.20827; PMID: 22688648
  • Chen L-L, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 2009; 35:467 - 78; http://dx.doi.org/10.1016/j.molcel.2009.06.027; PMID: 19716791
  • Elbarbary RA, Li W, Tian B, Maquat LE. STAU1 binding 3′ UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. Genes Dev 2013; 27:1495 - 510; http://dx.doi.org/10.1101/gad.220962.113; PMID: 23824540
  • Chen C, Ara T, Gautheret D. Using Alu elements as polyadenylation sites: A case of retroposon exaptation. Mol Biol Evol 2009; 26:327 - 34; http://dx.doi.org/10.1093/molbev/msn249; PMID: 18984903
  • Lee JY, Ji Z, Tian B. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes. Nucleic Acids Res 2008; 36:5581 - 90; http://dx.doi.org/10.1093/nar/gkn540; PMID: 18757892
  • Kim DS, Hahn Y. Identification of human-specific transcript variants induced by DNA insertions in the human genome. Bioinformatics 2011; 27:14 - 21; http://dx.doi.org/10.1093/bioinformatics/btq612; PMID: 21037245
  • Daskalova E, Baev V, Rusinov V, Minkov I. 3’UTR-located ALU elements: donors of potential miRNA target sites and mediators of network miRNA-based regulatory interactions. Evol Bioinform Online 2006; 2:103 - 20; PMID: 19455205
  • Lehnert S, Van Loo P, Thilakarathne PJ, Marynen P, Verbeke G, Schuit FC. Evidence for co-evolution between human microRNAs and Alu-repeats. PLoS One 2009; 4:e4456; http://dx.doi.org/10.1371/journal.pone.0004456; PMID: 19209240
  • Smalheiser NR, Torvik VI. A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions. BMC Bioinformatics 2004; 5:139; http://dx.doi.org/10.1186/1471-2105-5-139; PMID: 15453917
  • Liu WM, Chu WM, Choudary PV, Schmid CW. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 1995; 23:1758 - 65; http://dx.doi.org/10.1093/nar/23.10.1758; PMID: 7784180
  • Panning B, Smiley JR. Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6. Mol Cell Biol 1993; 13:3231 - 44; PMID: 7684492
  • Panning B, Smiley JR. Activation of RNA polymerase III transcription of human Alu elements by herpes simplex virus. Virology 1994; 202:408 - 17; http://dx.doi.org/10.1006/viro.1994.1357; PMID: 8009851
  • Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008; 29:499 - 509; http://dx.doi.org/10.1016/j.molcel.2007.12.013; PMID: 18313387
  • Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A 2009; 106:5569 - 74; http://dx.doi.org/10.1073/pnas.0810738106; PMID: 19307572
  • Wang J, Geesman GJ, Hostikka SL, Atallah M, Blackwell B, Lee E, Cook PJ, Pasaniuc B, Shariat G, Halperin E, et al. Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal. Cell Cycle 2011; 10:3016 - 30; http://dx.doi.org/10.4161/cc.10.17.17543; PMID: 21862875
  • Conley AB, Miller WJ, Jordan IK. Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 2008; 24:53 - 6; http://dx.doi.org/10.1016/j.tig.2007.11.008; PMID: 18192066
  • Osato N, Suzuki Y, Ikeo K, Gojobori T. Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics 2007; 176:1299 - 306; http://dx.doi.org/10.1534/genetics.106.069484; PMID: 17409075
  • Fire A. RNA-triggered gene silencing. Trends Genet 1999; 15:358 - 63; http://dx.doi.org/10.1016/S0168-9525(99)01818-1; PMID: 10461204
  • Hu Q, Tanasa B, Trabucchi M, Li W, Zhang J, Ohgi KA, Rose DW, Glass CK, Rosenfeld MG. DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol 2012; 19:1168 - 75; http://dx.doi.org/10.1038/nsmb.2400; PMID: 23064648
  • Chu WM, Ballard R, Carpick BW, Williams BR, Schmid CW. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 1998; 18:58 - 68; PMID: 9418853
  • Rubin CM, Kimura RH, Schmid CW. Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res 2002; 30:3253 - 61; http://dx.doi.org/10.1093/nar/gkf419; PMID: 12136107
  • Bovia F, Fornallaz M, Leffers H, Strub K. The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs. Mol Biol Cell 1995; 6:471 - 84; http://dx.doi.org/10.1091/mbc.6.4.471; PMID: 7542942
  • Chang DY, Hsu K, Maraia RJ. Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells. Nucleic Acids Res 1996; 24:4165 - 70; http://dx.doi.org/10.1093/nar/24.21.4165; PMID: 8932367
  • Hoffman Y, Dahary D, Bublik DR, Oren M, Pilpel Y. The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery. Bioinformatics 2013; 29:894 - 902; http://dx.doi.org/10.1093/bioinformatics/btt044; PMID: 23361327
  • Gong C, Maquat LE. “Alu”strious long ncRNAs and their role in shortening mRNA half-lives. Cell Cycle 2011; 10:1882 - 3; http://dx.doi.org/10.4161/cc.10.12.15589; PMID: 21487233
  • 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

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