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Zhang P, Mbodj A, Soundiramourtty A, Llauro C, Ghesquière A, Ingouff M, Keith Slotkin R, Pontvianne F, Catoni M, Mirouze M. Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants. Nat Commun 2023; 14:5236. [PMID: 37640706 PMCID: PMC10462705 DOI: 10.1038/s41467-023-41023-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
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.
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Affiliation(s)
- Panpan Zhang
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Montpellier, Montpellier, France
| | - Assane Mbodj
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
| | - Abirami Soundiramourtty
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Perpignan, Perpignan, France
| | - Christel Llauro
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Alain Ghesquière
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Mathieu Ingouff
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Frédéric Pontvianne
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France.
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France.
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Jamge B, Lorković ZJ, Axelsson E, Osakabe A, Shukla V, Yelagandula R, Akimcheva S, Kuehn AL, Berger F. Histone variants shape chromatin states in Arabidopsis. eLife 2023; 12:RP87714. [PMID: 37467143 PMCID: PMC10393023 DOI: 10.7554/elife.87714] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Akihisa Osakabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-kuTokyoJapan
- PRESTO, Japan Science and Technology Agency, HonchoKawaguchiJapan
| | - Vikas Shukla
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3ViennaAustria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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Berger F. Histone variants: The architects of chromatin. Semin Cell Dev Biol 2022; 135:1-2. [PMID: 35779977 DOI: 10.1016/j.semcdb.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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