DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates

Malicki, Marek; Spaller, Thomas; Winckler, Thomas; Hammann, Christian

doi:10.1093/nar/gkaa160

Cited by 8 publications

(4 citation statements)

References 65 publications

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“…We also identified conserved thymine trinucleotides (“TTT”) at the 5’ and 3’ ends in the complete copies of the DIRS-like elements of the genomes. This may be a general pattern of the DIRS-like elements found in terminal regions, which may be essential for transposing these elements (Malicki et al 2020). A similar terminal signature has also been described in the case of the DrDIRS1 element of Tribolium castaneum , which has either the trinucleotides ‘‘GTT’’ or dinucleotides “AA” (Goodwin et al 2004).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Gazolla

Ludwig

Gama

et al. 2021

Preprint

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Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in the X. laevis. X. tropicalis showed more recent amplification waves estimated around 16 mya and 3.2 mya and corroborate with high diversity-level of families in this species and with transcriptional activity evidence. Ngaro-like elements presented less diversity and quantity in the genomes, although potentially active copies were also found. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in the diploid X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process

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Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Gazolla

Ludwig

Gama

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…We also identified conserved thymine trinucleotides (“TTT”) at the 5′ and 3′ ends in the complete copies of the DIRS-like elements of the genomes. This is probably a general pattern of the DIRS - like elements found in terminal regions, which may be essential for transposing these elements ( Malicki et al 2020 ). A similar terminal signature has also been described for the DrDIRS1 element of Tribolium castaneum , which has either the trinucleotides “GTT” or dinucleotides “AA” ( Goodwin et al 2004 ).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Gazolla

Ludwig

Gama

et al. 2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17–18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' noncoding terminal regions, preserved open reading frames, and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.

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“…Most SINEs are derived from tRNA, 7SL RNA, or 5s RNA and have an RNA-Pol III promoter 45 , 46 . DIRS retrotransposons, which have tyrosine recombinase, differ from integrases or endonucleases commonly used by retrotransposons for site-specific genomic integration 47 , 48 . PLEs share an ancestor with telomerase reverse transcriptases (TERTs) and have unique features in retroelement phylogeny 49 .…”

Section: Introductionmentioning

confidence: 99%

Repetitive DNA sequence detection and its role in the human genome

Liao,

Zhu,

Zhou

et al. 2023

Commun Biol

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Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

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DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates

Cited by 8 publications

References 65 publications

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Repetitive DNA sequence detection and its role in the human genome

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