Distribution Of Retrotransposons Research Articles

Diversity Chromosome Evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH

Pennisetum purpureum is a potential species for biofuel production. Characterization and chromosomal distribution of retrotransposons could enhance the comprehension of the role and dynamics of the repetitive elements in plants. In this study, a phylogenetic tree was constructed according to the conserved reverse transcriptase sequences and revealed that these Ty1-copia retrotransposons had a typical structure. Analysis showed that the total Ty1-copia retrotransposons had a significant component, as high as 5.12 × 103 copy numbers in P. purpureum. Then, the chromosomal pattern of four known lineages were also analyzed with the Pennisetum glaucum genome, which suggested that the Sire/Maximus lineage had the highest copy number and followed by Tork/Angela, Tork/TAR, Retrofit/Ale. Additionally, the chromosomal distribution of total Ty1-copia retrotransposons was detected by fluorescence in situ hybridization (FISH) to be a dispersed pattern with weak clustering, mostly near the centromeric regions of P. purpureum chromosomes; interestingly, there were four obvious signals in the subterminal chromosomes. These results suggested that there occurred differential dynamic evolution directions of Ty1-copia retrotransposons within P. purpureum. Furthermore, co-localization of Ty1-copia, 5S rDNA, and 35S rDNA indicated that two chromosome 2 and four chromosome 4 were identified. Concurrently, subterminal signals of Ty1-copia-type retrotransposons were located on four other homologous chromosomes. Altogether, these results shed light on the diversification of Ty1-copia retrotransposons and have the significance for generation of valid chromosomal markers in retrotransposon families.

Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals.

The factors guiding retrotransposon insertion site preference are not well understood. Different types of retrotransposons share common replication machinery and yet occupy distinct genomic domains. Autonomous long interspersed elements accumulate in gene-poor domains and their nonautonomous short interspersed elements accumulate in gene-rich domains. To determine genomic factors that contribute to this discrepancy we analyzed the distribution of retrotransposons within the framework of chromosomal domains and regulatory elements. Using comparative genomics, we identified large-scale conserved patterns of retrotransposon accumulation across several mammalian genomes. Importantly, retrotransposons that were active after our sample-species diverged accumulated in orthologous regions. This suggested a similar evolutionary interaction between retrotransposon activity and conserved genome architecture across our species. In addition, we found that retrotransposons accumulated at regulatory element boundaries in open chromatin, where accumulation of particular retrotransposon types depended on insertion size and local regulatory element density. From our results, we propose a model where density and distribution of genes and regulatory elements canalize retrotransposon accumulation. Through conservation of synteny, gene regulation and nuclear organization, mammalian genomes with dissimilar retrotransposons follow similar evolutionary trajectories.

LTR retrotransposons cause expression changes of adjacent genes in early generations of the newly formed allotetraploid Cucumis hytivus

Cucumis hytivus is a newly synthesized allotetraploid in which retrotransposons was strongly activated owing to allopolyploidization. In present study, the chromosomal distribution of LTR retrotransposons and their effects on expression of adjacent genes were observed by investigating the first four generations of C. hytivus. Fluorescent in situ hybridization (FISH) analysis revealed that LTR retrotransposons are distributed throughout all the chromosomes. The clusters on terminal regions indicated the high copy number of retrotransposons in C. hytivus. The extensive epigenetic changes (gene silencing and gene activation) were detected by cDNA-SSAP analysis. Totally, twenty transcripts subjected to gene expression alterations were sequenced, including 12 gene silencing and 8 gene activation. However, the silenced/activated transcripts consisted of known genes or putative proteins as well as new sequences that had no similarity to any known genes. Both gene silencing and activation mainly occurred in the early generations of allotetraploid. The interlaced distribution of retrotransposons and genes might lead to the transcriptional interference of retrotransposons on expression of their adjacent genes, which may contribute to the rapid genetic stabilization of newly formed allotetraploid.

Linear decay of retrotransposon antisense bias across genes is contingent upon tissue specificity.

Retrotransposons comprise approximately half of the human genome and contribute to chromatin structure, regulatory motifs, and protein-coding sequences. Since retrotransposon insertions can disrupt functional genetic elements as well as introduce new sequence motifs to a region, they have the potential to affect the function of genes that harbour insertions as well as those nearby. Partly as a result of these effects, the distribution of retrotransposons across the genome is non-uniform and there are observed imbalances in the orientation of insertions with respect to the transcriptional direction of the containing gene. Although some of the factors underlying the observed distributions are understood, much of the variability remains unexplained. Detailed characterization of retrotransposon density in genes could help inform predictions of the functional consequence of de novo as well as polymorphic insertions. In order to characterize the relationship between genes and inserted elements, we have examined the distribution of retrotransposons and their internal motifs within tissue-specific and housekeeping genes. We have identified that the previously established retrotransposon antisense bias decays at a linear rate across genes, resulting in an equal density of sense and antisense retrotransposons near the 3′-UTR. In addition, the decay of antisense bias across genes is less pronounced among tissue-specific genes. Our results provide support for the scenario in which this linear decay in antisense bias is established by natural selection shortly after retrotransposon integration, and that total antisense bias observed is above and beyond any bias introduced by the integration process itself. Finally, we provide an example of a retrotransposon acting as an eQTL on a coincident gene, highlighting one of several possible avenues through which insertions may modulate gene function.

Chromosome organization of Ty1-copia-like retrotransposons in the tomato genome

Ty1-copia-like retrotransposons were discovered in all studied plants and form a considerable fraction of their genomes. PCR amplification of a pool of fragments of the reverse transcriptase gene of Ty1-copia-like retrotransposons of the tomato genome was conducted and their physical organization in mitotic and meiotic chromosomes was studied. The method of fluorescence in situ hybridization revealed the location of retrotransposons in the pericentromeric heterochromatin and their absence in the nucleolus organizer region. Knowledge of physical distribution of retrotransposons in the tomato genome is important when constructing molecular markers on their basis. Comparative analysis of chromosomal location of retrotransposons in different plant species extends our knowledge of the plant genome evolution.

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome.

Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.

Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome

An analysis of the distribution and age of LTR retrotransposons in the Arabidopsis genome revealed that Pseudoviridae insert randomly along the chromosome and have been recently active whereas Metaviridae were more active in the past and preferentially target heterochromatin.

Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.

Significant differences in levels of copia [Drosophila long terminal repeat (LTR) retrotransposon] expression exist among six species representing the Drosophila melanogaster species complex (D. melanogaster, Drosophila mauritiana, Drosophila simulans, Drosophila sechellia, Drosophila yakuba, and Drosophila erecta) and a more distantly related species (Drosophila willistoni). These differences in expression are correlated with major size variation mapping to putative regulatory regions of the copia 5' LTR and adjacent untranslated leader region (ULR). Sequence analysis indicates that these size variants were derived from a series of regional duplication events. The ability of the copia LTR-ULR size variants to drive expression of a bacterial chloramphenicol acetyltransferase reporter gene was tested in each of the seven species. The results indicate that both element-encoded (cis) and host-genome-encoded (trans) genetic differences are responsible for the variability in copia expression within and between Drosophila species. This finding indicates that models purporting to explain the dynamics and distribution of retrotransposons in natural populations must consider the potential impact of both element-encoded and host-genome-encoded regulatory variation to be valid. We propose that interelement selection among retrotransposons may provide a molecular drive mechanism for the evolution of eukaryotic enhancers which can be subsequently distributed throughout the genome by retrotransposition.