1
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Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38762905 DOI: 10.1111/pbi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
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Affiliation(s)
- Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiao Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Yutong Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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2
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [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: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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3
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Du J, Kim K, Chen M. Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations. Nat Commun 2024; 15:3620. [PMID: 38684657 PMCID: PMC11058242 DOI: 10.1038/s41467-024-47789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.
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Affiliation(s)
- Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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4
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Sakamoto T, Matsunaga S. Chromatin dynamics and subnuclear gene positioning for transcriptional regulation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102431. [PMID: 37562088 DOI: 10.1016/j.pbi.2023.102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response to environmental stresses. Regulation of specific chromatin positions in the nuclear space is important for transcription, and the mechanisms that enable such chromatin dynamics are gradually being unveiled. Genes move between subdomains responsible for transcriptional activation or suppression in the subnuclear space in a gene repositioning cycle. We propose a model of localized chromatin interaction in nuclear subdomains, in which the dynamics of local chromatin interactions have a more important impact on the regulation of gene expression than large-scale chromatin organization. In this mini-review, we highlight recent findings on chromatin dynamics, particularly involving transcriptional regulation, and discuss future directions in the study of chromatin organization in plants.
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Affiliation(s)
- Takuya Sakamoto
- Department of Science, Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-0802, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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5
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Hummel G, Liu C. Organization and epigenomic control of RNA polymerase III-transcribed genes in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102199. [PMID: 35364484 DOI: 10.1016/j.pbi.2022.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The genetic information linearly scripted in chromosomes is wrapped in a ribonucleoprotein complex called chromatin. The adaptation of its compaction level and spatiotemporal organization refines gene expression in response to developmental and environmental cues. RNA polymerase III (RNAPIII) is responsible for the biogenesis of elementary non-coding RNAs. Their genes are subjected to high duplication and mutational rates, and invade nuclear genomes. Their insertion into different epigenomic environments raises the question of how chromatin packing affects their individual transcription. In this review, we provide a unique perspective to this issue in plants. In addition, we discuss how the genomic organization of RNAPIII-transcribed loci, combined with epigenetic differences, might participate to plant trait variations.
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Affiliation(s)
- Guillaume Hummel
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany.
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany.
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6
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Domb K, Wang N, Hummel G, Liu C. Spatial Features and Functional Implications of Plant 3D Genome Organization. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:173-200. [PMID: 35130445 DOI: 10.1146/annurev-arplant-102720-022810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.
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Affiliation(s)
- Katherine Domb
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Guillaume Hummel
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
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7
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Tatout C, Mougeot G, Parry G, Baroux C, Pradillo M, Evans D. The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1926-1933. [PMID: 35090020 PMCID: PMC8982392 DOI: 10.1093/jxb/erac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
This Community Resource paper introduces the range of materials developed by the INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) COST Action made available through the INDEPTH Academy. Recent rapid growth in understanding of the significance of epigenetic controls in plant and crop science has led to a need for shared, high-quality resources, standardization of protocols, and repositories for open access data. The INDEPTH Academy provides a range of masterclass tutorials, standardized protocols, and teaching webinars, together with a rapidly developing repository to support imaging and spatial analysis of the nucleus and deep learning for automated analysis. These resources were developed partly as a response to the COVID-19 pandemic, but also driven by needs and opportunities identified by the INDEPTH community of ~200 researchers in 80 laboratories from 32 countries. This community report outlines the resources produced and how they will be extended beyond the INDEPTH project, but also aims to encourage the wider community to engage with epigenetics and nuclear structure by accessing these resources.
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Affiliation(s)
- Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
| | - Guillaume Mougeot
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Geraint Parry
- GARNet, Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Arabidopsis Events UK, 13 Mayhurst Ave, Woking GU22 8DE, UK
| | - Célia Baroux
- Zürich-Basel Plant Science Center, Department for Plant and Microbial Biology, University of Zürich, Switzerland
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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8
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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9
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Lei Z, Wang L, Kim EY, Cho J. Phase separation of chromatin and small RNA pathways in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1256-1265. [PMID: 34585805 DOI: 10.1111/tpj.15517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/18/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid-liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.
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Affiliation(s)
- Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Chinese Academy of Sciences, Shanghai, 200032, China
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10
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Di Stefano M, Nützmann HW. Modeling the 3D genome of plants. Nucleus 2021; 12:65-81. [PMID: 34057011 PMCID: PMC8168717 DOI: 10.1080/19491034.2021.1927503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.
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Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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11
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Baroux C. Three-dimensional genome organization in epigenetic regulations: cause or consequence? CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102031. [PMID: 33819713 DOI: 10.1016/j.pbi.2021.102031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The evolution of the nucleus is an evolutionary milestone. By enabling genome compartmentalization, it contributes to the fine-tuning of genome functions. The genome is partitioned into functional domains differing in spatial positioning and topological folding at different scales. The rise of '3D Genomics' embracing experimental, theoretical, and modeling approaches allowed the proposal of a multiscale model of the eukaryotic genome, capturing its organizing principles and functionalities. In these efforts, resolving causality remains an important objective. Are positioning and folding the cause or consequence of functional states? This minireview presents emerging answers to this question, borrowing examples from recent studies of the three-dimensional genome in both plants and animals.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Switzerland.
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12
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Farrona S, Mozgová I, Archacki R, Casas-Mollano JA. Editorial: Chromatin Stability and Dynamics: Targeting and Recruitment of Chromatin Modifiers. FRONTIERS IN PLANT SCIENCE 2021; 12:678702. [PMID: 34135931 PMCID: PMC8201073 DOI: 10.3389/fpls.2021.678702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Sara Farrona
- Plant and Agricultural Biosciences Centre-Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
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13
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Bishop J, Swan H, Valente F, Nützmann HW. The Plant Nuclear Envelope and Its Role in Gene Transcription. FRONTIERS IN PLANT SCIENCE 2021; 12:674209. [PMID: 33995467 PMCID: PMC8119737 DOI: 10.3389/fpls.2021.674209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/25/2021] [Indexed: 05/12/2023]
Abstract
Chromosomes are dynamic entities in the eukaryotic nucleus. During cell development and in response to biotic and abiotic change, individual sections as well as entire chromosomes re-organise and reposition within the nuclear space. A focal point for these processes is the nuclear envelope (NE) providing both barrier and anchor for chromosomal movement. In plants, positioning of chromosome regions and individual genes at the nuclear envelope has been shown to be associated with distinct transcriptional patterns. Here, we will review recent findings on the interplay between transcriptional activity and gene positioning at the nuclear periphery (NP). We will discuss potential mechanisms of transcriptional regulation at the nuclear envelope and outline future perspectives in this research area.
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14
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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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15
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Picart-Picolo A, Grob S, Picault N, Franek M, Llauro C, Halter T, Maier TR, Jobet E, Descombin J, Zhang P, Paramasivan V, Baum TJ, Navarro L, Dvořáčková M, Mirouze M, Pontvianne F. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome Res 2020; 30:1583-1592. [PMID: 33033057 PMCID: PMC7605254 DOI: 10.1101/gr.261586.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.
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Affiliation(s)
- Ariadna Picart-Picolo
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Stefan Grob
- Institute of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Nathalie Picault
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Christel Llauro
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Thierry Halter
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Edouard Jobet
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Julie Descombin
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Panpan Zhang
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | | | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Lionel Navarro
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Marie Mirouze
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | - Frédéric Pontvianne
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
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16
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Parry G, Pradillo M, Probst AV, Tatout C. Untangling chromatin interactions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5115-5118. [PMID: 32803270 DOI: 10.1093/jxb/eraa334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
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