tRNAs as primers and inhibitors of retrotransposons

References

• Mita P, Boeke JD. How retrotransposons shape genome regulation. Curr Opin Genet Dev. 2016;37:90–100. doi:10.1016/j.gde.2016.01.001. PMID:26855260
   PubMed Web of Science ®Google Scholar
• Levin HL, Moran JV. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet. 2011;12:615–27. doi:10.1038/nrg3030. PMID:21850042
   PubMed Web of Science ®Google Scholar
• Piegu B, Bire S, Arensburger P, Bigot Y. A survey of transposable element classification systems-a call for a fundamental update to meet the challenge of their diversity and complexity. Mol Phylogenet Evol. 2015;86:90–109. doi:10.1016/j.ympev.2015.03.009. PMID:25797922
   PubMed Web of Science ®Google Scholar
• Finnegan DJ. Retrotransposons. Curr Biol. 2012;22:R432–7. doi:10.1016/j.cub.2012.04.025. PMID:22677280
   PubMed Web of Science ®Google Scholar
• Havecker ER, Gao X, Voytas DF. The diversity of LTR retrotransposons. Genome Biol. 2004;5:225. doi:10.1186/gb-2004-5-6-225. PMID:15186483
   PubMed Web of Science ®Google Scholar
• Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8:272–85. doi:10.1038/nrg2072. PMID:17363976
   PubMed Web of Science ®Google Scholar
• Kelly NJ, Palmer MT, Morrow CD. Selection of Retroviral Reverse Transcription Primer Is Coordinated with tRNA Biogenesis. J Virol. 2003;77:8695–701. doi:10.1128/JVI.77.16.8695-8701.2003. PMID:12885888
   PubMed Web of Science ®Google Scholar
• Miller SB, Yildiz FZ, Lo JA, Wang B, D'Souza VM. A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Nature. 2014;515:591–5. doi:10.1038/nature13709. PMID:25209668
   PubMed Web of Science ®Google Scholar
• Mak J, Kleiman L. Primer tRNAs for reverse transcription. J Virol. 1997;71:8087–95. PMID:9343157
   PubMed Web of Science ®Google Scholar
• Flavell AJ. Retroelements, reverse transcriptase and evolution. Comp Biochem Physiol B Biochem Mol Biol. 1995;110:3–15. doi:10.1016/0305-0491(94)00122-B. PMID:7532085
   PubMed Web of Science ®Google Scholar
• Marquet R, Isel C, Ehresmann C, Ehresmann B. tRNAs as primer of reverse transcriptases. Biochimie. 1995;77:113–24. doi:10.1016/0300-9084(96)88114-4. PMID:7541250
   PubMed Web of Science ®Google Scholar
• Beerens N, Groot F, Berkhout B. Initiation of HIV-1 Reverse Transcription Is Regulated by a Primer Activation Signal. J Biol Chem. 2001;276:31247–56. doi:10.1074/jbc.M102441200. PMID:11384976
   PubMed Web of Science ®Google Scholar
• Telesnitsky A, Wolin SL. The Host RNAs in Retroviral Particles. Viruses. 2016;8:E235. doi:10.3390/v8080235. PMID:27548206
   PubMed Web of Science ®Google Scholar
• Rhim H, Park J, Morrow CD. Deletions in the tRNA(Lys) primer-binding site of human immunodeficiency virus type 1 identify essential regions for reverse transcription. J Virol. 1991;65:4555–64. PMID:1714513
   PubMed Web of Science ®Google Scholar
• Wilhelm M, Wilhelm FX. Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci. 2001;58:1246–62. doi:10.1007/PL00000937. PMID:11577982
   PubMed Web of Science ®Google Scholar
• Slotkin RK. The epigenetic control of the Athila family of retrotransposons in Arabidopsis. Epigenetics. 2010;5:483–90. doi:10.4161/epi.5.6.12119. PMID:20484989
   PubMed Web of Science ®Google Scholar
• Martinez G, Choudury SG, Slotkin RK. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Res. 2017;45:5142–52. doi:10.1093/nar/gkx103. PMID:28335016
   PubMed Web of Science ®Google Scholar
• Schorn AJ, Gutbrod MJ, LeBlanc C, Martienssen R. LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell. 2017;170:61–71 e11. doi:10.1016/j.cell.2017.06.013. PMID:28666125
   PubMed Web of Science ®Google Scholar
• Dhahbi JM. 5' tRNA Halves: The Next Generation of Immune Signaling Molecules. Front Immunol. 2015;6:74. doi:10.3389/fimmu.2015.00074. PMID:25745425
   PubMed Web of Science ®Google Scholar
• Pederson T. Regulatory RNAs derived from transfer RNA? RNA. 2010;16:1865–9. doi:10.1261/rna.2266510. PMID:20719919
   PubMed Web of Science ®Google Scholar
• Wang Y, Li H, Sun Q, Yao Y. Characterization of Small RNAs Derived from tRNAs, rRNAs and snoRNAs and Their Response to Heat Stress in Wheat Seedlings. PLoS One. 2016;11:e0150933. doi:10.1371/journal.pone.0150933. PMID:26963812
   PubMed Web of Science ®Google Scholar
• Thompson DM, Parker R. Stressing out over tRNA cleavage. Cell. 2009;138:215–9. doi:10.1016/j.cell.2009.07.001. PMID:19632169
   PubMed Web of Science ®Google Scholar
• Zhang S, Sun L, Kragler F. The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol. 2009;150:378–87. doi:10.1104/pp.108.134767. PMID:19261735
   PubMed Web of Science ®Google Scholar
• Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol. 2012;19:900–5. doi:10.1038/nsmb.2357. PMID:22885326
   PubMed Web of Science ®Google Scholar
• Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J. 2014;33:2020–39. doi:10.15252/embj.201489282. PMID:25063673
   PubMed Web of Science ®Google Scholar
• Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014;12:78. doi:10.1186/s12915-014-0078-0. PMID:25270025
   PubMed Web of Science ®Google Scholar
• Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009;136:461–72. doi:10.1016/j.cell.2008.12.038. PMID:19203581
   PubMed Web of Science ®Google Scholar
• Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell. 2012;151:194–205. doi:10.1016/j.cell.2012.09.001. PMID:23000270
   PubMed Web of Science ®Google Scholar
• Ibarra CA, Feng X, Schoft VK, Hsieh TF, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337:1360–4. doi:10.1126/science.1224839. PMID:22984074
   PubMed Web of Science ®Google Scholar
• Schoft VK, Chumak N, Mosiolek M, Slusarz L, Komnenovic V, Brownfield L, Twell D, Kakutani T, Tamaru H. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 2009;10:1015–21. doi:10.1038/embor.2009.152. PMID:19680290
   PubMed Web of Science ®Google Scholar
• Garcia-Lopez J, Hourcade Jde D, Alonso L, Cardenas DB, del Mazo J. Global characterization and target identification of piRNAs and endo-siRNAs in mouse gametes and zygotes. Biochim Biophys Acta. 2014;1839:463–75. doi:10.1016/j.bbagrm.2014.04.006. PMID:24769224
   PubMed Web of Science ®Google Scholar
• Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016;351:391–6. doi:10.1126/science.aad6780. PMID:26721685
   PubMed Web of Science ®Google Scholar
• Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, Broday L, Pilpel Y, Rechavi O. Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. PLoS Genet. 2016;12:e1006264. doi:10.1371/journal.pgen.1006264. PMID:27560950
   PubMed Web of Science ®Google Scholar
• Gingold H, Tehler D, Christoffersen NR, Nielsen MM, Asmar F, Kooistra SM, Christophersen NS, Christensen LL, Borre M, Sørensen KD, et al. A dual program for translation regulation in cellular proliferation and differentiation. Cell. 2014;158:1281–92. doi:10.1016/j.cell.2014.08.011. PMID:25215487
   PubMed Web of Science ®Google Scholar
• Hasler D, Lehmann G, Murakawa Y, Klironomos F, Jakob L, Grasser FA, Rajewsky N, Landthaler M, Meister G. The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway. Mol Cell. 2016;63:110–24. doi:10.1016/j.molcel.2016.05.026. PMID:27345152
   PubMed Web of Science ®Google Scholar
• Zuo Z, Peng D, Yin X, Zhou X, Cheng H, Zhou R. Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves. Mol Biol Evol. 2013;30:2087–98. doi:10.1093/molbev/mst107. PMID:23744908
   PubMed Web of Science ®Google Scholar
• Phizicky EM, Hopper AK. tRNA biology charges to the front. Genes Dev. 2010;24:1832–60. doi:10.1101/gad.1956510. PMID:20810645
   PubMed Web of Science ®Google Scholar