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Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
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Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
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Meschichi A, Zhao L, Reeck S, White C, Da Ines O, Sicard A, Pontvianne F, Rosa S. The plant-specific DDR factor SOG1 increases chromatin mobility in response to DNA damage. EMBO Rep 2022; 23:e54736. [PMID: 36278395 PMCID: PMC9724665 DOI: 10.15252/embr.202254736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observe an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. This increase in mobility is lost in the sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Also, DSB sites show particularly high mobility levels and their enhanced mobility requires the HR factor RAD54. Our data suggest that repair mechanisms promote chromatin mobility upon DNA damage, implying a role of this process in the early steps of the DNA damage response.
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Affiliation(s)
- Anis Meschichi
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Lihua Zhao
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Svenja Reeck
- John Innes Centre, Norwich Research ParkNorwichUK
| | - Charles White
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Adrien Sicard
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP)Université de Perpignan Via DomitiaPerpignanFrance
| | - Stefanie Rosa
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
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Payne-Dwyer AL, Leake MC. Single-Molecular Quantification of Flowering Control Proteins Within Nuclear Condensates in Live Whole Arabidopsis Root. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2476:311-328. [PMID: 35635712 DOI: 10.1007/978-1-0716-2221-6_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here we describe the coupled standardization of two complementary fluorescence imaging techniques and apply it to liquid-liquid phase-separated condensates formed from an EGFP fluorescent reporter of flowering control locus A (FCA), a protein that associates with chromosomal DNA in plants during epigenetic regulation of the flowering process. First, we use home-built single-molecule Slimfield microscopy to establish a fluorescent protein standard. This sample comprises live yeast cells expressing Mig1 protein, a metabolic regulator which localizes to the nucleus under conditions of high glucose, fused to the same type of EGFP label as for the FCA fusion construct. Then we employ commercial confocal AiryScan microscopy to study the same standard. Finally, we demonstrate how to quantify FCA-EGFP nuclear condensates in intact root tips at rapid timescales and apply this calibration. This method is a valuable approach to obtaining single-molecule precise stoichiometry and copy number estimates of protein condensates that are integrated into the chromosome architecture of plants, using confocal instrumentation that lacks de facto single-molecule detection sensitivity.
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Affiliation(s)
- Alex L Payne-Dwyer
- Department of Physics, University of York, York, UK.
- Departments of Physics and Biology, University of York, York, UK.
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S, Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F. ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta. FRONTIERS IN PLANT SCIENCE 2021; 12:677849. [PMID: 34295343 PMCID: PMC8290188 DOI: 10.3389/fpls.2021.677849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/09/2021] [Indexed: 05/05/2023]
Abstract
Together with local chromatin structure, gene accessibility, and the presence of transcription factors, gene positioning is implicated in gene expression regulation. Although the basic mechanisms are expected to be conserved in eukaryotes, less is known about the role of gene positioning in plant cells, mainly due to the lack of a highly resolutive approach. In this study, we adapted the use of the ANCHOR system to perform real-time single locus detection in planta. ANCHOR is a DNA-labeling tool derived from the chromosome partitioning system found in many bacterial species. We demonstrated its suitability to monitor a single locus in planta and used this approach to track chromatin mobility during cell differentiation in Arabidopsis thaliana root epidermal cells. Finally, we discussed the potential of this approach to investigate the role of gene positioning during transcription and DNA repair in plants.
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Affiliation(s)
- Anis Meschichi
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Claire Picart
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Marie Mirouze
- Université de Montpellier, DIADE, Montpellier, France
- Institut de Recherche pour le Développement, DIADE, Montpellier, France
| | - Sophie Desset
- iGReD, CNRS UMR 6293, Université Clermont Auvergne, INSERM U1103, Clermont–Ferrand, France
| | | | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Nathalie Picault
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
- *Correspondence: Frédéric Pontvianne
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