Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements

Volff, Jean‐Nicolas; Hornung, Ute; Schartl, Manfred

doi:10.1007/s004380100468

Cited by 51 publications

(11 citation statements)

References 42 publications

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“…Like in trematodes, motifs could be grouped in consensus families, and for each genome, only a few examples mapped within full PLEs. Regarding vertebrates, similar min-HHRs were found within Xena , Poseidon , and Neptune PLEs from diverse fishes ( Volff et al 2001 ; Dalle Nogare et al 2002 ), but also widespread throughout the genomes ( fig. 2 B ).…”

Section: Resultsmentioning

confidence: 71%

Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

Cervera

Peña

2014

Molecular Biology and Evolution

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Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

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Section: Resultsmentioning

confidence: 71%

Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

Cervera

Peña

2014

Molecular Biology and Evolution

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“…The Penelope retrotransposons encode a single ORF composed of the RT and EN domains. The latter is similar to GIY-YIG intron-encoded ENs (2,30,84,121), named after the conserved amino acid motif Gly-Ile-Tyr-Xn-Tyr-Ile-Gly. It appears that the Penelope RT is closer to telomerases and bacterial RTs than RTs encoded by non-LTR retrotransposons (2).…”

Section: Non-long Terminal Repeat and Long Terminal Repeat Retrotransmentioning

confidence: 94%

Repetitive Sequences in Complex Genomes: Structure and Evolution

Jurka

Kapitonov

Kohany

et al. 2007

Annu. Rev. Genom. Hum. Genet.

334

289

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Eukaryotic genomes contain vast amounts of repetitive DNA derived from transposable elements (TEs). Large-scale sequencing of these genomes has produced an unprecedented wealth of information about the origin, diversity, and genomic impact of what was once thought to be "junk DNA." This has also led to the identification of two new classes of DNA transposons, Helitrons and Polintons, as well as several new superfamilies and thousands of new families. TEs are evolutionary precursors of many genes, including RAG1, which plays a role in the vertebrate immune system. They are also the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic stability and evolution. Remnants of TEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation.

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“…Because of its long terminal repeats, it was considered expediently as a member of the LTR retrotransposons, although its features differ from other LTR retrotransposons that are described above. The presence of GIY-YIG-type endonuclease downstream of the RT domain led to a new definition of Penelope and its relatives as a new group of retrotransposons (Lyozin et al, 2001;Volff et al, 2001). This GIY-YIG endonuclease works analogously to APE and RLE in non-LTR retrotransposons; Penelope-like elements likely transpose via the TPRT mechanism (Pyatkov et al, 2004).…”

Section: Cr1 Groupmentioning

confidence: 99%

Structural and sequence diversity of eukaryotic transposable elements

Kojima

2019

Genes Genet. Syst.

102

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The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation. In this review, our current understanding regarding the diversity of eukaryotic TEs in sequence, protein domain composition and structural hallmarks is introduced and summarized, based on the classification system implemented in Repbase. Autonomous eukaryotic TEs can be divided into two groups: Class I TEs, also called retrotransposons, and Class II TEs, or DNA transposons. Long terminal repeat (LTR) retrotransposons, including endogenous retroviruses, non-LTR retrotransposons, tyrosine recombinase retrotransposons and Penelope-like elements, are well accepted groups of autonomous retrotransposons. They share reverse transcriptase for replication but are distinct in the catalytic components responsible for integration into the host genome. Similarly, at least three transposition machineries have been reported in eukaryotic DNA transposons: DDD/E transposase, tyrosine recombinase and HUH endonuclease combined with helicase. Among these, TEs with DDD/E transposase are dominant and are classified into 21 superfamilies in Repbase. Non-autonomous TEs are either simple derivatives generated by internal deletion, or are composed of several units that originated independently.

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Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements

Cited by 51 publications

References 42 publications

Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

Repetitive Sequences in Complex Genomes: Structure and Evolution

Structural and sequence diversity of eukaryotic transposable elements

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