A tale of an A-tail

References

• Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, et al. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genet 2012; 8:e1002842; http://dx.doi.org/10.1371/journal.pgen.1002842; PMID: 22912586
   PubMed Web of Science ®Google Scholar
• Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, et al. Under the genomic radar: the stealth model of Alu amplification. Genome Res 2005; 15:655 - 64; http://dx.doi.org/10.1101/gr.3492605; PMID: 15867427
   PubMed Web of Science ®Google Scholar
• Walker JA, Konkel MK, Ullmer B, Monceaux CP, Ryder OA, Hubley R, et al. Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. Mob DNA 2012; 3:8; http://dx.doi.org/10.1186/1759-8753-3-8; PMID: 22541534
   PubMedGoogle Scholar
• Kopera HC, Moldovan JB, Morrish TA, Garcia-Perez JL, Moran JV. Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase. Proc Natl Acad Sci U S A 2011; 108:20345 - 50; http://dx.doi.org/10.1073/pnas.1100275108; PMID: 21940498
   PubMed Web of Science ®Google Scholar
• Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 2003; 35:41 - 8; http://dx.doi.org/10.1038/ng1223; PMID: 12897783
   PubMed Web of Science ®Google Scholar
• Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, et al. Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci U S A 2006; 103:17620 - 5; http://dx.doi.org/10.1073/pnas.0605421103; PMID: 17101970
   PubMed Web of Science ®Google Scholar
• 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
• Graham T, Boissinot S. The genomic distribution of L1 elements: the role of insertion bias and natural selection. J Biomed Biotechnol 2006; 2006:75327; http://dx.doi.org/10.1155/JBB/2006/75327; PMID: 16877820
   PubMed Web of Science ®Google Scholar
• Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, et al. Mobile elements create structural variation: analysis of a complete human genome. Genome Res 2009; 19:1516 - 26; http://dx.doi.org/10.1101/gr.091827.109; PMID: 19439515
   PubMed Web of Science ®Google Scholar
• Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, et al. 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
   PubMed Web of Science ®Google Scholar
• Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, et al, 1000 Genomes Project. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet 2011; 7:e1002236; http://dx.doi.org/10.1371/journal.pgen.1002236; PMID: 21876680
   PubMed Web of Science ®Google Scholar
• Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 2001; 21:1429 - 39; http://dx.doi.org/10.1128/MCB.21.4.1429-1439.2001; PMID: 11158327
   PubMed Web of Science ®Google Scholar
• Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al, Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520 - 62; http://dx.doi.org/10.1038/nature01262; PMID: 12466850
   PubMed Web of Science ®Google Scholar
• Gonçalves I, Duret L, Mouchiroud D. Nature and structure of human genes that generate retropseudogenes. Genome Res 2000; 10:672 - 8; http://dx.doi.org/10.1101/gr.10.5.672; PMID: 10810090
   PubMed Web of Science ®Google Scholar
• Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003; 4:R74; http://dx.doi.org/10.1186/gb-2003-4-11-r74; PMID: 14611660
   PubMedGoogle Scholar
• Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 2000; 24:363 - 7; http://dx.doi.org/10.1038/74184; PMID: 10742098
   PubMed Web of Science ®Google Scholar
• Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, et al. SVA elements: a hominid-specific retroposon family. J Mol Biol 2005; 354:994 - 1007; http://dx.doi.org/10.1016/j.jmb.2005.09.085; PMID: 16288912
   PubMed Web of Science ®Google Scholar
• Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH Jr.. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 2011; 20:3386 - 400; http://dx.doi.org/10.1093/hmg/ddr245; PMID: 21636526
   PubMed Web of Science ®Google Scholar
• Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, et al. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 2011; PMID: 22053090
   PubMed Web of Science ®Google Scholar
• Ohshima K, Hamada M, Terai Y, Okada N. The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol Cell Biol 1996; 16:3756 - 64; PMID: 8668192
   PubMed Web of Science ®Google Scholar
• Kajikawa M, Okada N. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 2002; 111:433 - 44; http://dx.doi.org/10.1016/S0092-8674(02)01041-3; PMID: 12419252
   PubMed Web of Science ®Google Scholar
• Terai Y, Takahashi K, Okada N. SINE cousins: the 3′-end tails of the two oldest and distantly related families of SINEs are descended from the 3′ ends of LINEs with the same genealogical origin. Mol Biol Evol 1998; 15:1460 - 71; http://dx.doi.org/10.1093/oxfordjournals.molbev.a025873; PMID: 12572609
   PubMed Web of Science ®Google Scholar
• Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 1993; 72:595 - 605; http://dx.doi.org/10.1016/0092-8674(93)90078-5; PMID: 7679954
   PubMed Web of Science ®Google Scholar
• Luan DD, Eickbush TH. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol 1995; 15:3882 - 91; PMID: 7540721
   PubMed Web of Science ®Google Scholar
• Boeke JD. LINEs and Alus--the polyA connection. Nat Genet 1997; 16:6 - 7; http://dx.doi.org/10.1038/ng0597-6; PMID: 9140383
   PubMed Web of Science ®Google Scholar
• Dewannieux M, Heidmann T. Role of poly(A) tail length in Alu retrotransposition. Genomics 2005; 86:378 - 81; http://dx.doi.org/10.1016/j.ygeno.2005.05.009; PMID: 15993034
   PubMed Web of Science ®Google Scholar
• Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr.. High frequency retrotransposition in cultured mammalian cells. Cell 1996; 87:917 - 27; http://dx.doi.org/10.1016/S0092-8674(00)81998-4; PMID: 8945518
   PubMed Web of Science ®Google Scholar
• Keller W. No end yet to messenger RNA 3′ processing!. Cell 1995; 81:829 - 32; http://dx.doi.org/10.1016/0092-8674(95)90001-2; PMID: 7781059
   PubMed Web of Science ®Google Scholar
• Borodulina OR, Kramerov DA. Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure. Mamm Genome 2001; 12:779 - 86; http://dx.doi.org/10.1007/s003350020029; PMID: 11668393
   PubMed Web of Science ®Google Scholar
• Borodulina OR, Kramerov DA. Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner. RNA 2008; 14:1865 - 73; http://dx.doi.org/10.1261/rna.1006608; PMID: 18658125
   PubMed Web of Science ®Google Scholar
• Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005; 247:165 - 221; http://dx.doi.org/10.1016/S0074-7696(05)47004-7; PMID: 16344113
   PubMed Web of Science ®Google Scholar
• Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411 - 27; http://dx.doi.org/10.1007/s00439-005-1321-0; PMID: 15983781
   PubMed Web of Science ®Google Scholar
• Walter P, Blobel G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 1982; 299:691 - 8; http://dx.doi.org/10.1038/299691a0; PMID: 6181418
   PubMed Web of Science ®Google Scholar
• Gogolevsky KP, Vassetzky NS, Kramerov DA. 5S rRNA-derived and tRNA-derived SINEs in fruit bats. Genomics 2009; 93:494 - 500; http://dx.doi.org/10.1016/j.ygeno.2009.02.001; PMID: 19442632
   PubMed Web of Science ®Google Scholar
• Nishihara H, Terai Y, Okada N. Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins. Mol Biol Evol 2002; 19:1964 - 72; http://dx.doi.org/10.1093/oxfordjournals.molbev.a004020; PMID: 12411605
   PubMed Web of Science ®Google Scholar
• Daniels GR, Deininger PL. Repeat sequence families derived from mammalian tRNA genes. Nature 1985; 317:819 - 22; http://dx.doi.org/10.1038/317819a0; PMID: 3851163
   PubMed Web of Science ®Google Scholar
• Chen Y, Sinha K, Perumal K, Gu J, Reddy R. Accurate 3′ end processing and adenylation of human signal recognition particle RNA and alu RNA in vitro. J Biol Chem 1998; 273:35023 - 31; http://dx.doi.org/10.1074/jbc.273.52.35023; PMID: 9857035
   PubMed Web of Science ®Google Scholar
• Sinha K, Perumal K, Chen Y, Reddy R. Post-transcriptional adenylation of signal recognition particle RNA is carried out by an enzyme different from mRNA Poly(A) polymerase. J Biol Chem 1999; 274:30826 - 31; http://dx.doi.org/10.1074/jbc.274.43.30826; PMID: 10521474
   PubMed Web of Science ®Google Scholar
• White RJ. RNA polymerases I and III, non-coding RNAs and cancer. Trends Genet 2008; 24:622 - 9; http://dx.doi.org/10.1016/j.tig.2008.10.003; PMID: 18980784
   PubMed Web of Science ®Google Scholar
• Anderson JT, Wang X. Nuclear RNA surveillance: no sign of substrates tailing off. Crit Rev Biochem Mol Biol 2009; 44:16 - 24; http://dx.doi.org/10.1080/10409230802640218; PMID: 19280429
   PubMed Web of Science ®Google Scholar
• Houseley J, Tollervey D. The many pathways of RNA degradation. Cell 2009; 136:763 - 76; http://dx.doi.org/10.1016/j.cell.2009.01.019; PMID: 19239894
   PubMed Web of Science ®Google Scholar
• Kadaba S, Wang X, Anderson JT. Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 2006; 12:508 - 21; http://dx.doi.org/10.1261/rna.2305406; PMID: 16431988
   PubMed Web of Science ®Google Scholar
• Copela LA, Fernandez CF, Sherrer RL, Wolin SL. Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation. RNA 2008; 14:1214 - 27; http://dx.doi.org/10.1261/rna.1050408; PMID: 18456844
   PubMed Web of Science ®Google Scholar
• LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005; 121:713 - 24; http://dx.doi.org/10.1016/j.cell.2005.04.029; PMID: 15935758
   PubMed Web of Science ®Google Scholar
• Vanácová S, Wolf J, Martin G, Blank D, Dettwiler S, Friedlein A, et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 2005; 3:e189; http://dx.doi.org/10.1371/journal.pbio.0030189; PMID: 15828860
   PubMed Web of Science ®Google Scholar
• Schneider C, Anderson JT, Tollervey D. The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 2007; 27:324 - 31; http://dx.doi.org/10.1016/j.molcel.2007.06.006; PMID: 17643380
   PubMed Web of Science ®Google Scholar
• Wlotzka W, Kudla G, Granneman S, Tollervey D. The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J 2011; 30:1790 - 803; http://dx.doi.org/10.1038/emboj.2011.97; PMID: 21460797
   PubMed Web of Science ®Google Scholar
• Jia H, Wang X, Liu F, Guenther UP, Srinivasan S, Anderson JT, et al. The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. Cell 2011; 145:890 - 901; http://dx.doi.org/10.1016/j.cell.2011.05.010; PMID: 21663793
   PubMed Web of Science ®Google Scholar
• Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, et al. Active Alu element “A-tails”: size does matter. Genome Res 2002; 12:1333 - 44; http://dx.doi.org/10.1101/gr.384802; PMID: 12213770
   PubMed Web of Science ®Google Scholar
• Okada N, Hamada M, Ogiwara I, Ohshima K. SINEs and LINEs share common 3′ sequences: a review. Gene 1997; 205:229 - 43; http://dx.doi.org/10.1016/S0378-1119(97)00409-5; PMID: 9461397
   PubMed Web of Science ®Google Scholar