[ James A. Shapiro ] James A. Shapiro


LTR retrotransposons and genome evolution

(Kuff, Feenstra et al. 1983; Pedersen, Paludan et al. 1991; Lyden, Johnson et al. 1994; Wessler, Bureau et al. 1995; McDonald, Matyunina et al. 1997; Dunn, Medstrand et al. 2003; Scholes, Kenny et al. 2003; Dewannieux, Dupressoir et al. 2004; Semin and Il'in Iu 2005; Vitte and Panaud 2005; Desmarais, Belkhir et al. 2006; Kovalskaya, Buzdin et al. 2006; Sin, Huh et al. 2006; Maisonhaute, Ogereau et al. 2007; Piriyapongsa, Polavarapu et al. 2007; Rho, Choi et al. 2007; Romanish, Lock et al. 2007; Vitte, Panaud et al. 2007; Faye, Arnaud et al. 2008; Fukai, Dobrowolska et al. 2008; Huh, Kim et al. 2008; Novikova, Mayorov et al. 2008; Wang and Liu 2008; Zolotukhin, Schneider et al. 2008; Baucom, Estill et al. 2009; Cohen, Lock et al. 2009; Kuykendall, Shao et al. 2009; Li, Slife et al. 2009; Llorens, Munoz-Pomer et al. 2009; Macas, Koblizkova et al. 2009; Minervini, Viggiano et al. 2009; Novikova 2009; Du, Tian et al. 2010; Konovalov, Goncharov et al. 2010; Makunin and Iurlova 2010; Mourier and Willerslev 2010; Ragupathy, Banks et al. 2010; Sreenath, Pavithra et al. 2010; Zedek, Smerda et al. 2010; Liu and Eiden 2011; Muszewska, Hoffman-Sommer et al. 2011; Salina, Sergeeva et al. 2011; Zaratiegui, Vaughn et al. 2011; Marsano, Leronni et al. 2012; Sun, Shepard et al. 2012)

 

REFERENCES

 

Baucom, R. S., J. C. Estill, et al. (2009). "Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome." Genome Res 19(2): 243-254. http://www.ncbi.nlm.nih.gov/pubmed/19029538.

Cohen, C. J., W. M. Lock, et al. (2009). "Endogenous retroviral LTRs as promoters for human genes: a critical assessment." Gene 448(2): 105-114. http://www.ncbi.nlm.nih.gov/pubmed/19577618.

Desmarais, E., K. Belkhir, et al. (2006). "Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome." J Mol Evol 63(5): 662-675. http://www.ncbi.nlm.nih.gov/pubmed/17075698.

Dewannieux, M., A. Dupressoir, et al. (2004). "Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells." Nat Genet 36(5): 534-539. http://www.ncbi.nlm.nih.gov/pubmed/15107856.

Du, J., Z. Tian, et al. (2010). "Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison." Plant J 63(4): 584-598. http://www.ncbi.nlm.nih.gov/pubmed/20525006.

Dunn, C. A., P. Medstrand, et al. (2003). "An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon." Proc Natl Acad Sci U S A 100(22): 12841-12846. http://www.ncbi.nlm.nih.gov/pubmed/14534330.

Faye, B., F. Arnaud, et al. (2008). "Functional characteristics of a highly specific integrase encoded by an LTR-retrotransposon." PLoS One 3(9): e3185. http://www.ncbi.nlm.nih.gov/pubmed/18784842.

Fukai, E., A. D. Dobrowolska, et al. (2008). "Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus." Plant Mol Biol 68(6): 653-663. http://www.ncbi.nlm.nih.gov/pubmed/18802778.

Huh, J. W., D. S. Kim, et al. (2008). "Transcriptional regulation of GSDML gene by antisense-oriented HERV-H LTR element." Arch Virol 153(6): 1201-1205. http://www.ncbi.nlm.nih.gov/pubmed/18478180.

Konovalov, F. A., N. P. Goncharov, et al. (2010). "Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats." Mol Genet Genomics 283(6): 551-563. http://www.ncbi.nlm.nih.gov/pubmed/20407790.

Kovalskaya, E., A. Buzdin, et al. (2006). "Functional human endogenous retroviral LTR transcription start sites are located between the R and U5 regions." Virology 346(2): 373-378. http://www.ncbi.nlm.nih.gov/pubmed/16337666.

Kuff, E. L., A. Feenstra, et al. (1983). "Homology between an endogenous viral LTR and sequences inserted in an activated cellular oncogene." Nature 302(5908): 547-548. http://www.ncbi.nlm.nih.gov/pubmed/6835385.

Kuykendall, D., J. Shao, et al. (2009). "A Nest of LTR Retrotransposons Adjacent the Disease Resistance-Priming Gene NPR1 in Beta vulgaris L. U.S. Hybrid H20." Int J Plant Genomics 2009: 576742. http://www.ncbi.nlm.nih.gov/pubmed/19390694.

Li, X., J. Slife, et al. (2009). "Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao." BMC Evol Biol 9: 128. http://www.ncbi.nlm.nih.gov/pubmed/19500371.

Liu, M. and M. V. Eiden (2011). "Role of human endogenous retroviral long terminal repeats (LTRs) in maintaining the integrity of the human germ line." Viruses 3(6): 901-905. http://www.ncbi.nlm.nih.gov/pubmed/21994760.

Llorens, C., A. Munoz-Pomer, et al. (2009). "Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees." Biol Direct 4: 41. http://www.ncbi.nlm.nih.gov/pubmed/19883502.

Lyden, T. W., P. M. Johnson, et al. (1994). "Ultrastructural characterization of endogenous retroviral particles isolated from normal human placentas." Biol Reprod 51(1): 152-157. http://www.ncbi.nlm.nih.gov/pubmed/7522592.

Macas, J., A. Koblizkova, et al. (2009). "Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats." Gene 448(2): 198-206. http://www.ncbi.nlm.nih.gov/pubmed/19563868.

Maisonhaute, C., D. Ogereau, et al. (2007). "Amplification of the 1731 LTR retrotransposon in Drosophila melanogaster cultured cells: origin of neocopies and impact on the genome." Gene 393(1-2): 116-126. http://www.ncbi.nlm.nih.gov/pubmed/17382490.

Makunin, I. V. and A. A. Iurlova (2010). "[LTR retrotransposons as a source of promoters in the Drosophila genome]." Genetika 46(9): 1202-1204. http://www.ncbi.nlm.nih.gov/pubmed/21061618.

Marsano, R. M., D. Leronni, et al. (2012). "Mosquitoes LTR retrotransposons: a deeper view into the genomic sequence of Culex quinquefasciatus." PLoS One 7(2): e30770. http://www.ncbi.nlm.nih.gov/pubmed/22383973.

McDonald, J. F., L. V. Matyunina, et al. (1997). "LTR retrotransposons and the evolution of eukaryotic enhancers." Genetica 100(1-3): 3-13. http://www.ncbi.nlm.nih.gov/pubmed/9440254.

Minervini, C. F., L. Viggiano, et al. (2009). "Identification of novel LTR retrotransposons in the genome of Aedes aegypti." Gene 440(1-2): 42-49. http://www.ncbi.nlm.nih.gov/pubmed/19362135.

Mourier, T. and E. Willerslev (2010). "Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons." BMC Genomics 11: 167. http://www.ncbi.nlm.nih.gov/pubmed/20226011.

Muszewska, A., M. Hoffman-Sommer, et al. (2011). "LTR retrotransposons in fungi." PLoS One 6(12): e29425. http://www.ncbi.nlm.nih.gov/pubmed/22242120.

Novikova, O. (2009). "Chromodomains and LTR retrotransposons in plants." Commun Integr Biol 2(2): 158-162. http://www.ncbi.nlm.nih.gov/pubmed/19513271.

Novikova, O., V. Mayorov, et al. (2008). "Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta)." Plant J 56(4): 562-574. http://www.ncbi.nlm.nih.gov/pubmed/18643967.

Pedersen, F. S., K. Paludan, et al. (1991). "The murine leukemia virus LTR in oncogenesis: effect of point mutations and chromosomal integration sites." Radiat Environ Biophys 30(3): 195-197. http://www.ncbi.nlm.nih.gov/pubmed/1656479.

Piriyapongsa, J., N. Polavarapu, et al. (2007). "Exonization of the LTR transposable elements in human genome." BMC Genomics 8: 291. http://www.ncbi.nlm.nih.gov/pubmed/17725822.

Ragupathy, R., T. Banks, et al. (2010). "Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome." Mol Genet Genomics 283(3): 255-271. http://www.ncbi.nlm.nih.gov/pubmed/20127492.

Rho, M., J. H. Choi, et al. (2007). "De novo identification of LTR retrotransposons in eukaryotic genomes." BMC Genomics 8: 90. http://www.ncbi.nlm.nih.gov/pubmed/17407597.

Romanish, M. T., W. M. Lock, et al. (2007). "Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution." PLoS Genet 3(1): e10. http://www.ncbi.nlm.nih.gov/pubmed/17222062.

Salina, E. A., E. M. Sergeeva, et al. (2011). "The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats." BMC Plant Biol 11: 99. http://www.ncbi.nlm.nih.gov/pubmed/21635794.

Scholes, D. T., A. E. Kenny, et al. (2003). "Activation of a LTR-retrotransposon by telomere erosion." Proc Natl Acad Sci U S A 100(26): 15736-15741. http://www.ncbi.nlm.nih.gov/pubmed/14673098.

Semin, B. V. and V. Il'in Iu (2005). "[Diversity of LTR retrotransposons and their role in genome reorganization]." Genetika 41(4): 542-548. http://www.ncbi.nlm.nih.gov/pubmed/15909914.

Sin, H. S., J. W. Huh, et al. (2006). "Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells." Arch Virol 151(10): 1985-1994. http://www.ncbi.nlm.nih.gov/pubmed/16625320.

Sreenath, K., L. Pavithra, et al. (2010). "Nuclear matrix protein SMAR1 represses HIV-1 LTR mediated transcription through chromatin remodeling." Virology 400(1): 76-85. http://www.ncbi.nlm.nih.gov/pubmed/20153010.

Sun, C., D. B. Shepard, et al. (2012). "LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders." Genome Biol Evol 4(2): 168-183. http://www.ncbi.nlm.nih.gov/pubmed/22200636.

Vitte, C. and O. Panaud (2005). "LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model." Cytogenet Genome Res 110(1-4): 91-107. http://www.ncbi.nlm.nih.gov/pubmed/16093661.

Vitte, C., O. Panaud, et al. (2007). "LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss." BMC Genomics 8: 218. http://www.ncbi.nlm.nih.gov/pubmed/17617907.

Wang, H. and J. S. Liu (2008). "LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice." BMC Genomics 9: 382. http://www.ncbi.nlm.nih.gov/pubmed/18691433.

Wessler, S. R., T. E. Bureau, et al. (1995). "LTR-retrotransposons and MITEs: important players in the evolution of plant genomes." Curr Opin Genet Dev 5(6): 814-821. http://www.ncbi.nlm.nih.gov/pubmed/8745082.

Zaratiegui, M., M. W. Vaughn, et al. (2011). "CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR." Nature 469(7328): 112-115. .

Zedek, F., J. Smerda, et al. (2010). "Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis." BMC Plant Biol 10: 265. http://www.ncbi.nlm.nih.gov/pubmed/21118487.

Zolotukhin, A. S., R. Schneider, et al. (2008). "The RNA transport element RTE is essential for IAP LTR-retrotransposon mobility." Virology 377(1): 88-99. http://www.ncbi.nlm.nih.gov/pubmed/18485438.