Genomes and Genes
terminal repeat sequences
Summary: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.
- Zedek F, Smerda J, Smarda P, Bures P. Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol. 2010;10:265 pubmed publisher..We also examined how this relationship is reflected in the phylogeny of Eleocharis...
- Gimenez J, Montgiraud C, Oriol G, Pichon J, Ruel K, Tsatsaris V, et al. Comparative methylation of ERVWE1/syncytin-1 and other human endogenous retrovirus LTRs in placenta tissues. DNA Res. 2009;16:195-211 pubmed publisher..These results suggest that HERV methylation might not be family related but copy-specific, and related to the LTR function and the tissue. In particular, ERVWE1 and ERV3 could be developmentally epigenetically regulated HERVs...
- Majumdar A, Chatterjee A, Ripmaster T, Levin H. Determinants that specify the integration pattern of retrotransposon Tf1 in the fbp1 promoter of Schizosaccharomyces pombe. J Virol. 2011;85:519-29 pubmed publisher..Strains lacking each of these proteins revealed that Atf1p alone mediated the sites of integration. These data indicate that Atf1p plays a direct and specific role in targeting integration in the promoter of fbp1. ..
- Kalendar R, Antonius K, Smykal P, Schulman A. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet. 2010;121:1419-30 pubmed publisher..Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge. ..
- Kovach A, Wegrzyn J, Parra G, Holt C, Bruening G, Loopstra C, et al. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics. 2010;11:420 pubmed publisher..The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda...
- Delihas N. Impact of small repeat sequences on bacterial genome evolution. Genome Biol Evol. 2011;3:959-73 pubmed publisher..The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described. ..
- Cohen C, Lock W, Mager D. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene. 2009;448:105-14 pubmed publisher..We discuss these findings and offer evolutionary models to explain these trends. ..
- Ungerer M, Strakosh S, Stimpson K. Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data. BMC Biol. 2009;7:40 pubmed publisher..Temporal estimates of these proliferation events suggest an earlier origin for these hybrid species than previously supposed. ..
- Estep M, Debarry J, Bennetzen J. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity (Edinb). 2013;110:194-204 pubmed publisher..Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification...
- Kronmiller B, Wise R. Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. Plant Physiol. 2009;151:483-95 pubmed publisher..Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations...
- Kijima T, Innan H. On the estimation of the insertion time of LTR retrotransposable elements. Mol Biol Evol. 2010;27:896-904 pubmed publisher..It is concluded that the divergence method to estimate the insertion time should be applied with special caution because at least some LTRs undergo gene conversion. ..
- Steinbauerová V, Neumann P, Novak P, Macas J. A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. Genetica. 2011;139:1543-55 pubmed publisher..In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element. ..
- Hawkins J, Proulx S, Rapp R, Wendel J. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci U S A. 2009;106:17811-6 pubmed publisher..These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity. ..
- Tian Z, Rizzon C, Du J, Zhu L, Bennetzen J, Jackson S, et al. Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?. Genome Res. 2009;19:2221-30 pubmed publisher..Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome. ..
- Schön U, Diem O, Leitner L, Gunzburg W, Mager D, Salmons B, et al. Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. J Virol. 2009;83:12643-50 pubmed publisher..Our data show that HERV LTRs function in the context of retroviral vectors in certain cell types and have the potential to be useful as cell type-specific promoters in vector construction. ..
- Nystedt B, Street N, Wetterbom A, Zuccolo A, Lin Y, Scofield D, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497:579-84 pubmed publisher..We further identify numerous long (>10,000?base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding...
- Luchetti A, Mingazzini V, Mantovani B. 28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca). Genomics. 2012;100:51-6 pubmed publisher..The analysis of 28S/R2 5' end junctions further suggests aberrant homologous recombination, as observed in RNA viruses. ..
- Beyer U, Moll Rocek J, Moll U, Dobbelstein M. Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes. Proc Natl Acad Sci U S A. 2011;108:3624-9 pubmed publisher..By providing increased germ-line stability, this event may have contributed to the evolution of hominids and enabled their long reproductive periods...
- Nefedova L, Mannanova M, Kim A. Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome. Virus Genes. 2011;42:297-306 pubmed publisher..Chromodomain is present in the integrase structures of blastopia and 412 subgroup LTR-retrotransposons and may facilitate the process of non-specific integration. ..
- Fernández Medina R, Struchiner C, Ribeiro J. Novel transposable elements from Anopheles gambiae. BMC Genomics. 2011;12:260 pubmed publisher..This work contributes to a better understanding of the landscape of TEs present in the mosquito genome. It also presents a novel platform for the identification, analysis, and characterization of TEs on sequenced genomes. ..
- Blass E, Bell M, Boissinot S. Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Genome Biol Evol. 2012;4:687-702 pubmed publisher..We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions...
- Llorens C, Futami R, Covelli L, Domínguez Escribà L, Viu J, Tamarit D, et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2011;39:D70-4 pubmed publisher..GyDB 2.0 is available at http://gydb.org. ..
- Aurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, et al. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Hum Gene Ther Methods. 2012;23:18-28 pubmed publisher..Because this method can be used universally for all AAV2 genome-based vectors, it will significantly simplify rAAV2 vector titrations in the future. ..
- Jurka J, Bao W, Kojima K. Families of transposable elements, population structure and the origin of species. Biol Direct. 2011;6:44 pubmed publisher..The hypothesis also has implications for the ongoing debate on the role of genetic drift in genome evolution. ..
- Kapitonov V, Tempel S, Jurka J. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene. 2009;448:207-13 pubmed publisher..5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1). ..
- Ravimohan S, Gama L, Barber S, Clements J. Regulation of SIV mac 239 basal long terminal repeat activity and viral replication in macrophages: functional roles of two CCAAT/enhancer-binding protein beta sites in activation and interferon beta-mediated suppression. J Biol Chem. 2010;285:2258-73 pubmed publisher..In conjunction with previous studies from our laboratory, we demonstrate the importance of these sites in virus gene expression, and we propose a model for their role in establishing latency and persistence in macrophages in the brain...
- Weber B, Wenke T, Frömmel U, Schmidt T, Heitkam T. The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res. 2010;18:247-63 pubmed publisher..The analysis of two retrotransposons from the same subclass contrasting in abundance, age, sequence diversity, and localization gives insight in the heterogeneity of LTR retrotransposons populating a plant genome...
- Duc Dodon M, Mesnard J, Barbeau B. [Adult T-cell leukemia induced by HTLV-1: before and after HBZ]. Med Sci (Paris). 2010;26:391-6 pubmed publisher..Moreover, recent studies found that the viral HBZ gene was always expressed in leukemic cells, suggesting its involvement in the progression of the infected cells towards malignancy. ..
- Garcia Etxebarria K, Jugo B. Genome-wide detection and characterization of endogenous retroviruses in Bos taurus. J Virol. 2010;84:10852-62 pubmed publisher..This study demonstrates the importance of using multiple methods when trying to identify new ERVs and shows that the number of bovine ERV families is not as limited as previously thought...
- Park S, Huh J, Kim D, Ha H, Jung Y, Ahn K, et al. Analysis of the molecular and regulatory properties of active porcine endogenous retrovirus gamma-1 long terminal repeats in kidney tissues of the NIH-Miniature pig. Mol Cells. 2010;30:319-25 pubmed publisher..SssI. These data indicate that transcribed PERV LTR elements harbor sufficient promoter activity to regulate the transcription of a single virus, and the transcriptional activity of PERV LTRs may be controlled by DNA methylation events. ..
- Martins H, Villesen P. Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLoS ONE. 2011;6:e14745 pubmed publisher..For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible. ..
- Minervini C, Ruggieri S, Traversa M, D Aiuto L, Marsano R, Leronni D, et al. Evidences for insulator activity of the 5'UTR of the Drosophila melanogaster LTR-retrotransposon ZAM. Mol Genet Genomics. 2010;283:503-9 pubmed publisher..These results suggest the possibility of employing the ZAM insulator in gene transfer protocols from insects to mammals in order to counteract the transgene positional and genotoxic effects. ..
- Gimenez J, Montgiraud C, Pichon J, Bonnaud B, Arsac M, Ruel K, et al. Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control. Nucleic Acids Res. 2010;38:2229-46 pubmed publisher..The analysis of DNA from tumoral versus normal tissue revealed that hypomethylation of U3 promoters in tumors is a prerequisite for their activation. ..
- Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A. Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics. 2012;190:263-74 pubmed publisher..speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group. ..
- Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, et al. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS ONE. 2012;7:e32973 pubmed publisher..Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France. ..
- Venancio T, Wilson R, Verjovski Almeida S, DeMarco R. Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoni. Int J Parasitol. 2010;40:743-9 pubmed publisher..We hypothesise that these bursts could be a consequence of the evolutionary pressure resulting from migration of Schistosoma from Asia to Africa and their establishment in this new environment, helping both speciation and adaptation. ..
- Woolcock K, Gaidatzis D, Punga T, Buhler M. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol. 2011;18:94-9 pubmed publisher..We anticipate that similar mechanisms could also be operational in other eukaryotes. ..
- Steinbiss S, Willhoeft U, Gremme G, Kurtz S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 2009;37:7002-13 pubmed publisher..Representative sequences from 41 of these 62 groups were matched to reference sequences with >80% global sequence similarity. ..
- Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature. 2009;461:427-30 pubmed publisher..Our results demonstrate that epigenetic control of retrotransposons extends beyond transcriptional suppression and can be individualized for particular elements. ..
- Bleykasten Grosshans C, Jung P, Fritsch E, Potier S, De Montigny J, Souciet J. The Ty1 LTR-retrotransposon population in Saccharomyces cerevisiae genome: dynamics and sequence variations during mobility. FEMS Yeast Res. 2011;11:334-44 pubmed publisher..In this process, highly expressed and strikingly nonautonomous mutant Ty1 were found to be the most frequently used resident copies, which suggests that nonautonomous elements play a key role in the dynamics of the Ty1 family. ..
- Piednoël M, Carrete Vega G, Renner S. Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species. Plant J. 2013;75:699-709 pubmed publisher..Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae also revealed that the Bianca clade of Ty1/Copia and the SMART-related elements are much more widely distributed among angiosperms than previously known. ..