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Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally un...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7215508/ https://www.ncbi.nlm.nih.gov/pubmed/32331257 http://dx.doi.org/10.3390/ijms21082931 |
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author | Kalendar, Ruslan Raskina, Olga Belyayev, Alexander Schulman, Alan H. |
author_facet | Kalendar, Ruslan Raskina, Olga Belyayev, Alexander Schulman, Alan H. |
author_sort | Kalendar, Ruslan |
collection | PubMed |
description | Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established. |
format | Online Article Text |
id | pubmed-7215508 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-72155082020-05-22 Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants Kalendar, Ruslan Raskina, Olga Belyayev, Alexander Schulman, Alan H. Int J Mol Sci Article Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established. MDPI 2020-04-22 /pmc/articles/PMC7215508/ /pubmed/32331257 http://dx.doi.org/10.3390/ijms21082931 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Kalendar, Ruslan Raskina, Olga Belyayev, Alexander Schulman, Alan H. Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title | Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title_full | Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title_fullStr | Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title_full_unstemmed | Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title_short | Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants |
title_sort | long tandem arrays of cassandra retroelements and their role in genome dynamics in plants |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7215508/ https://www.ncbi.nlm.nih.gov/pubmed/32331257 http://dx.doi.org/10.3390/ijms21082931 |
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