The diversity of retrotransposons and the properties of their reverse transcriptases

Eickbush, Thomas H.; Jamburuthugoda, Varuni K.

doi:10.1016/j.virusres.2007.12.010

Cited by 218 publications

(193 citation statements)

References 116 publications

(145 reference statements)

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“…So, a single ORF with a central reverse transcriptase domain is present, as in type II non-LTR retrotransposons (Eickbush and Jamburuthugoda, 2008). In addition, its insertion site within the T. cancriformis 28S gene is the same as in all studied organisms Kojima and Fujiwara, 2005) save ticks, which show two nucleotide substitutions within the normal target sequence (Bunikis and Barbour, 2005).…”

Section: Discussionmentioning

confidence: 99%

R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution

2010

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The R2 retrotransposon is here characterized in bisexual populations of the European crustacean Triops cancriformis. The isolated element matches well with the general aspects of the R2 family and it is highly differentiated from that of the congeneric North American Triops longicaudatus. The analysis of 5 0 truncations indicates that R2 dynamics in T. cancriformis populations show a high turnover rate as observed in Drosophila simulans. For the first time in the literature, though, individuals harboring truncation variants, but lacking the complete element, are found. Present results suggest that transposition-mediated deletion mechanisms, possibly involving genomic turnover processes acting on rDNAs, can dramatically decrease the copy number or even delete R2 from the ribosomal locus. The presence of R2 does not seem to impact on the nucleotide variation of inserted 28S rDNA with respect to the uninserted genes. On the other hand, a low level of polymorphism characterizes rDNA units because new 28S variants continuously spread across the ribosomal array. Again, the interplay between transposition-mediated deletion and molecular drive may explain this pattern.

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Section: Discussionmentioning

confidence: 99%

R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution

2010

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“…Most L1 copies are truncated from the 59 end due to a nonprocessive reverse transcriptase activity during retrotransposition (Luan et al 1993;Ostertag and Kazazian 2000;Eickbush and Jamburuthugoda 2008). Therefore, any analysis that considers all genomic copies of a particular LINE family together results in a gross underestimation of the level of H3K9me3 signals on the 59 portions of full-length L1 elements.…”

Section: Distribution Of the H3k9me3 Mark On Different Repeat Classesmentioning

confidence: 99%

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells

et al. 2014

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Transposable elements (TEs) occupy a large fraction of metazoan genomes and pose a constant threat to genomic integrity. This threat is particularly critical in germ cells, as changes in the genome that are induced by TEs will be transmitted to the next generation. Small noncoding piwi-interacting RNAs (piRNAs) recognize and silence a diverse set of TEs in germ cells. In mice, piRNA-guided transposon repression correlates with establishment of CpG DNA methylation on their sequences, yet the mechanism and the spectrum of genomic targets of piRNA silencing are unknown. Here we show that in addition to DNA methylation, the piRNA pathway is required to maintain a high level of the repressive H3K9me3 histone modification on long interspersed nuclear elements (LINEs) in germ cells. piRNA-dependent chromatin repression targets exclusively full-length elements of actively transposing LINE families, demonstrating the remarkable ability of the piRNA pathway to recognize active elements among the large number of genomic transposon fragments.

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“…Because LTR retrotransposons are widely shared across species (Havecker et al 2004;Eickbush and Jamburuthugoda 2008), we searched additional animal genomes for signs of LTR-mediated retroposition. Specifically, we applied the pipeline used to identify recently originated retrocopies in Drosophila to five other species (mosquito, zebrafish, chicken, mouse, and human) representing a broad taxonomic breadth (Methods).…”

Section: Ltr Retrotransposons Mediate Retroposition Across Animalsmentioning

confidence: 99%

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

et al. 2016

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In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, L1 retrotransposons drive retroposition, but the elements responsible for retroposition in other animals have yet to be identified. Here, we examined young retrocopies from various animals that still retain the sequence features indicative of the underlying retroposition mechanism. In Drosophila melanogaster, we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short similar sequences that suggest the involvement of microsimilarity-dependent template switches. By expanding our approach to mosquito, zebrafish, chicken, and mammals, we identified in all these species recently originated retrocopies with a similar chimeric structure and shared microsimilarities at the fusion points. We also identified several retrocopies that combine the sequences of two or more parental genes, demonstrating LTR-retroposition as a novel mechanism of exon shuffling. Finally, we found that LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. Transcriptional profiling coupled with sequence analyses revealed that the sense-strand transcription of the retrocopies often lead to the origination of in-frame proteins relative to the parental genes. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa; combined with previous work from plants and yeast, it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.

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The diversity of retrotransposons and the properties of their reverse transcriptases

Cited by 218 publications

References 116 publications

R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution

R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

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