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Tandem repeats derived from centromeric retrotransposons
BACKGROUND: Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648361/ https://www.ncbi.nlm.nih.gov/pubmed/23452340 http://dx.doi.org/10.1186/1471-2164-14-142 |
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author | Sharma, Anupma Wolfgruber, Thomas K Presting, Gernot G |
author_facet | Sharma, Anupma Wolfgruber, Thomas K Presting, Gernot G |
author_sort | Sharma, Anupma |
collection | PubMed |
description | BACKGROUND: Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotransposons, are enriched at centromeres. Some satellite repeats have homology to retrotransposons and several mechanisms have been proposed to explain the expansion, contraction as well as homogenization of tandem repeats. However, the origin and evolution of tandem repeat loci remain largely unknown. RESULTS: CRM1TR and CRM4TR are novel tandem repeats that we show to be entirely derived from CR elements belonging to two different subfamilies, CRM1 and CRM4. Although these tandem repeats clearly originated in at least two separate events, they are derived from similar regions of their respective parent element, namely the long terminal repeat (LTR) and untranslated region (UTR). The 5(′) ends of the monomer repeat units of CRM1TR and CRM4TR map to different locations within their respective LTRs, while their 3(′) ends map to the same relative position within a conserved region of their UTRs. Based on the insertion times of heterologous retrotransposons that have inserted into these tandem repeats, amplification of the repeats is estimated to have begun at least ~4 (CRM1TR) and ~1 (CRM4TR) million years ago. Distinct CRM1TR sequence variants occupy the two CRM1TR loci, indicating that there is little or no movement of repeats between loci, even though they are separated by only ~1.4 Mb. CONCLUSIONS: The discovery of two novel retrotransposon derived tandem repeats supports the conclusions from earlier studies that retrotransposons can give rise to tandem repeats in eukaryotic genomes. Analysis of monomers from two different CRM1TR loci shows that gene conversion is the major cause of sequence variation. We propose that successive intrastrand deletions generated the initial repeat structure, and gene conversions increased the size of each tandem repeat locus. |
format | Online Article Text |
id | pubmed-3648361 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36483612013-05-09 Tandem repeats derived from centromeric retrotransposons Sharma, Anupma Wolfgruber, Thomas K Presting, Gernot G BMC Genomics Research Article BACKGROUND: Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotransposons, are enriched at centromeres. Some satellite repeats have homology to retrotransposons and several mechanisms have been proposed to explain the expansion, contraction as well as homogenization of tandem repeats. However, the origin and evolution of tandem repeat loci remain largely unknown. RESULTS: CRM1TR and CRM4TR are novel tandem repeats that we show to be entirely derived from CR elements belonging to two different subfamilies, CRM1 and CRM4. Although these tandem repeats clearly originated in at least two separate events, they are derived from similar regions of their respective parent element, namely the long terminal repeat (LTR) and untranslated region (UTR). The 5(′) ends of the monomer repeat units of CRM1TR and CRM4TR map to different locations within their respective LTRs, while their 3(′) ends map to the same relative position within a conserved region of their UTRs. Based on the insertion times of heterologous retrotransposons that have inserted into these tandem repeats, amplification of the repeats is estimated to have begun at least ~4 (CRM1TR) and ~1 (CRM4TR) million years ago. Distinct CRM1TR sequence variants occupy the two CRM1TR loci, indicating that there is little or no movement of repeats between loci, even though they are separated by only ~1.4 Mb. CONCLUSIONS: The discovery of two novel retrotransposon derived tandem repeats supports the conclusions from earlier studies that retrotransposons can give rise to tandem repeats in eukaryotic genomes. Analysis of monomers from two different CRM1TR loci shows that gene conversion is the major cause of sequence variation. We propose that successive intrastrand deletions generated the initial repeat structure, and gene conversions increased the size of each tandem repeat locus. BioMed Central 2013-03-04 /pmc/articles/PMC3648361/ /pubmed/23452340 http://dx.doi.org/10.1186/1471-2164-14-142 Text en Copyright © 2013 Sharma et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Sharma, Anupma Wolfgruber, Thomas K Presting, Gernot G Tandem repeats derived from centromeric retrotransposons |
title | Tandem repeats derived from centromeric retrotransposons |
title_full | Tandem repeats derived from centromeric retrotransposons |
title_fullStr | Tandem repeats derived from centromeric retrotransposons |
title_full_unstemmed | Tandem repeats derived from centromeric retrotransposons |
title_short | Tandem repeats derived from centromeric retrotransposons |
title_sort | tandem repeats derived from centromeric retrotransposons |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648361/ https://www.ncbi.nlm.nih.gov/pubmed/23452340 http://dx.doi.org/10.1186/1471-2164-14-142 |
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