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Survey of extrachromosomal circular DNA derived from plant satellite repeats
BACKGROUND: Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly un...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2543021/ https://www.ncbi.nlm.nih.gov/pubmed/18721471 http://dx.doi.org/10.1186/1471-2229-8-90 |
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author | Navrátilová, Alice Koblížková, Andrea Macas, Jiří |
author_facet | Navrátilová, Alice Koblížková, Andrea Macas, Jiří |
author_sort | Navrátilová, Alice |
collection | PubMed |
description | BACKGROUND: Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes. RESULTS: We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths. CONCLUSION: This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity. |
format | Text |
id | pubmed-2543021 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25430212008-09-19 Survey of extrachromosomal circular DNA derived from plant satellite repeats Navrátilová, Alice Koblížková, Andrea Macas, Jiří BMC Plant Biol Research Article BACKGROUND: Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes. RESULTS: We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths. CONCLUSION: This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity. BioMed Central 2008-08-22 /pmc/articles/PMC2543021/ /pubmed/18721471 http://dx.doi.org/10.1186/1471-2229-8-90 Text en Copyright © 2008 Navrátilová 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 Navrátilová, Alice Koblížková, Andrea Macas, Jiří Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title | Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title_full | Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title_fullStr | Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title_full_unstemmed | Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title_short | Survey of extrachromosomal circular DNA derived from plant satellite repeats |
title_sort | survey of extrachromosomal circular dna derived from plant satellite repeats |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2543021/ https://www.ncbi.nlm.nih.gov/pubmed/18721471 http://dx.doi.org/10.1186/1471-2229-8-90 |
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