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Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462705/ https://www.ncbi.nlm.nih.gov/pubmed/37640706 http://dx.doi.org/10.1038/s41467-023-41023-0 |
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author | Zhang, Panpan Mbodj, Assane Soundiramourtty, Abirami Llauro, Christel Ghesquière, Alain Ingouff, Mathieu Keith Slotkin, R. Pontvianne, Frédéric Catoni, Marco Mirouze, Marie |
author_facet | Zhang, Panpan Mbodj, Assane Soundiramourtty, Abirami Llauro, Christel Ghesquière, Alain Ingouff, Mathieu Keith Slotkin, R. Pontvianne, Frédéric Catoni, Marco Mirouze, Marie |
author_sort | Zhang, Panpan |
collection | PubMed |
description | Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants. |
format | Online Article Text |
id | pubmed-10462705 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-104627052023-08-30 Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants Zhang, Panpan Mbodj, Assane Soundiramourtty, Abirami Llauro, Christel Ghesquière, Alain Ingouff, Mathieu Keith Slotkin, R. Pontvianne, Frédéric Catoni, Marco Mirouze, Marie Nat Commun Article Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants. Nature Publishing Group UK 2023-08-28 /pmc/articles/PMC10462705/ /pubmed/37640706 http://dx.doi.org/10.1038/s41467-023-41023-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Zhang, Panpan Mbodj, Assane Soundiramourtty, Abirami Llauro, Christel Ghesquière, Alain Ingouff, Mathieu Keith Slotkin, R. Pontvianne, Frédéric Catoni, Marco Mirouze, Marie Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title | Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title_full | Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title_fullStr | Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title_full_unstemmed | Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title_short | Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants |
title_sort | extrachromosomal circular dna and structural variants highlight genome instability in arabidopsis epigenetic mutants |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462705/ https://www.ncbi.nlm.nih.gov/pubmed/37640706 http://dx.doi.org/10.1038/s41467-023-41023-0 |
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