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Amiard S, Feit L, Vanrobays E, Simon L, Le Goff S, Loizeau L, Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C, Probst AV. The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development. Plant Commun 2024:100890. [PMID: 38566416 DOI: 10.1016/j.xplc.2024.100890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/07/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plant-specific transcriptional regulators called TELOMERE REPEAT BINDING proteins (TRBs) combine two DNA-binding domains, the GH1 domain, which binds to linker DNA and is shared with H1 histones, and the Myb/SANT domain, which specifically recognizes the telobox DNA-binding site motif. TRB1, TRB2, and TRB3 proteins recruit Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at gene promoters containing telobox motifs to repress transcription. Here, we demonstrate that TRB4 and TRB5, two related paralogs belonging to a separate TRB clade conserved in spermatophytes, regulate the transcription of several hundred genes involved in developmental responses to environmental cues. Indeed, TRB4 binds to several thousand sites in the genome, mainly at TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but unlike TRB1 it is not enriched at H3K27me3-marked gene bodies. Yet, TRB4 can physically interact with the catalytic components of PRC2, SWINGER and CURLY LEAF (CLF). Unexpectedly, we show that TRB4 and TRB5 are required for distinctive phenotypic traits observed in clf mutant plants and accordingly function as transcriptional activators of several hundred of CLF-controlled genes, including key flowering genes. We further demonstrate that TRB4 shares multiple target genes with TRB1 and physically and genetically interacts with members of both TRB clades. Collectively, this study uncovers that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through both PRC2-dependent and independent mechanisms.
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Affiliation(s)
- Simon Amiard
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
| | - Léa Feit
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Samuel Le Goff
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Loriane Loizeau
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Léa Wolff
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Falk Butter
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Christophe Tatout
- 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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Mermet S, Voisin M, Mordier J, Dubos T, Tutois S, Tuffery P, Baroux C, Tamura K, Probst AV, Vanrobays E, Tatout C. Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores. Plant Cell 2023; 35:4284-4303. [PMID: 37738557 PMCID: PMC10689174 DOI: 10.1093/plcell/koad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/24/2023]
Abstract
The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear shape and gene expression. To understand how the Arabidopsis (Arabidopsis thaliana) nucleoskeleton physically connects to the nuclear periphery in plants, we investigated the Arabidopsis nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. We identified 3 conserved peptide motifs within the N-terminal region of KAKU4, which are required for intermolecular interactions of KAKU4 with itself, interaction with the nucleoskeleton protein CROWDED NUCLEI (CRWN), localization at the nuclear periphery, and nuclear elongation in differentiated tissues. Unexpectedly, we find these motifs to be present also in NUP82 and NUP136, 2 plant-specific nucleoporins from the nuclear pore basket. We further show that NUP82, NUP136, and KAKU4 have a common evolutionary history predating nonvascular land plants with KAKU4 mainly localizing outside the nuclear pore suggesting its divergence from an ancient nucleoporin into a new nucleoskeleton component. Finally, we demonstrate that both NUP82 and NUP136, through their shared N-terminal motifs, interact with CRWN and KAKU4 proteins revealing the existence of a physical continuum between the nuclear pore and the nucleoskeleton in plants.
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Affiliation(s)
- Sarah Mermet
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Maxime Voisin
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Joris Mordier
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Tristan Dubos
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Sylvie Tutois
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Pierre Tuffery
- Université Paris Cité, CNRS UMR 8251, INSERM ERL U1133, 75013 Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Aline V Probst
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Christophe Tatout
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
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Andov B, Boulaflous-Stevens A, Pain C, Mermet S, Voisin M, Charrondiere C, Vanrobays E, Tutois S, Evans DE, Kriechbaumer V, Tatout C, Graumann K. In Depth Topological Analysis of Arabidopsis Mid-SUN Proteins and Their Interaction with the Membrane-Bound Transcription Factor MaMYB. Plants (Basel) 2023; 12:plants12091787. [PMID: 37176845 PMCID: PMC10180911 DOI: 10.3390/plants12091787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Mid-SUN proteins are a neglected family of conserved type III membrane proteins of ancient origin with representatives in plants, animals, and fungi. Previous higher plant studies have associated them with functions at the nuclear envelope and the endoplasmic reticulum (ER). In this study, high-resolution confocal light microscopy is used to explore the localisation of SUN3 and SUN4 in the perinuclear region, to explore topology, and to study the role of mid-SUNs on endoplasmic reticulum morphology. The role of SUN3 in the ER is reinforced by the identification of a protein interaction between SUN3 and the ER membrane-bound transcription factor maMYB. The results highlight the importance of mid-SUNs as functional components of the ER and outer nuclear membrane.
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Affiliation(s)
- Bisa Andov
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | | | - Charlotte Pain
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Sarah Mermet
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Maxime Voisin
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Camille Charrondiere
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Sylvie Tutois
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - David E Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Verena Kriechbaumer
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christophe Tatout
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Katja Graumann
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus 2022; 13:277-299. [PMID: 36447428 PMCID: PMC9754023 DOI: 10.1080/19491034.2022.2144013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
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Affiliation(s)
- Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Anna Nowicka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Kateřina Kaduchová
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Michaela Kubová
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Mohammad A. Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Christophe Tatout
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Isabelle Colas
- The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, Scotland UK
| | | | - Sophie Desset
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Sarah Mermet
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Aurélia Boulaflous-Stevens
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | | | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Devin Routh
- Service and Support for Science IT (S3IT), Universität Zürich, Zürich, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland,CONTACT Célia Baroux Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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Dubos T, Poulet A, Thomson G, Péry E, Chausse F, Tatout C, Desset S, van Wolfswinkel JC, Jacob Y. NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects. BMC Bioinformatics 2022; 23:216. [PMID: 35668354 PMCID: PMC9169307 DOI: 10.1186/s12859-022-04743-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization. RESULTS We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest. CONCLUSION AND AVAILABILITY NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis . The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE .
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Affiliation(s)
- Tristan Dubos
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Geoffrey Thomson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Emilie Péry
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Frédéric Chausse
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Desset
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
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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. J Exp Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mougeot G, Dubos T, Chausse F, Péry E, Graumann K, Tatout C, Evans DE, Desset S. Deep learning -- promises for 3D nuclear imaging: a guide for biologists. J Cell Sci 2022; 135:275041. [PMID: 35420128 PMCID: PMC9016621 DOI: 10.1242/jcs.258986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
For the past century, the nucleus has been the focus of extensive investigations in cell biology. However, many questions remain about how its shape and size are regulated during development, in different tissues, or during disease and aging. To track these changes, microscopy has long been the tool of choice. Image analysis has revolutionized this field of research by providing computational tools that can be used to translate qualitative images into quantitative parameters. Many tools have been designed to delimit objects in 2D and, eventually, in 3D in order to define their shapes, their number or their position in nuclear space. Today, the field is driven by deep-learning methods, most of which take advantage of convolutional neural networks. These techniques are remarkably adapted to biomedical images when trained using large datasets and powerful computer graphics cards. To promote these innovative and promising methods to cell biologists, this Review summarizes the main concepts and terminologies of deep learning. Special emphasis is placed on the availability of these methods. We highlight why the quality and characteristics of training image datasets are important and where to find them, as well as how to create, store and share image datasets. Finally, we describe deep-learning methods well-suited for 3D analysis of nuclei and classify them according to their level of usability for biologists. Out of more than 150 published methods, we identify fewer than 12 that biologists can use, and we explain why this is the case. Based on this experience, we propose best practices to share deep-learning methods with biologists.
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Affiliation(s)
- Guillaume Mougeot
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France.,Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Tristan Dubos
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Frédéric Chausse
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, F-63000 Clermont-Ferrand, France
| | - Emilie Péry
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, F-63000 Clermont-Ferrand, France
| | - Katja Graumann
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - David E Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Sophie Desset
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
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Dubos T, Poulet A, Gonthier-Gueret C, Mougeot G, Vanrobays E, Li Y, Tutois S, Pery E, Chausse F, Probst AV, Tatout C, Desset S. Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0. Nucleus 2021; 11:315-329. [PMID: 33153359 PMCID: PMC7714466 DOI: 10.1080/19491034.2020.1845012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at https://www.brookes.ac.uk/indepth/images/ . Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence in situ hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.
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Affiliation(s)
- Tristan Dubos
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Axel Poulet
- Department of Molecular, Cellular & Developmental Biology, Yale University , New Haven, CT, USA
| | | | - Guillaume Mougeot
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University , Oxford, UK
| | - Emmanuel Vanrobays
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Yanru Li
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich , Zürich, Switzerland
| | - Sylvie Tutois
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Emilie Pery
- Institut Pascal, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Frédéric Chausse
- Institut Pascal, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Aline V Probst
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Sophie Desset
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
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9
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Abstract
In this review, we explore recent advances in knowledge of the structure and dynamics of the plant nuclear envelope. As a paradigm, we focused our attention on the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, a structurally conserved bridging complex comprising SUN domain proteins in the inner nuclear membrane and KASH domain proteins in the outer nuclear membrane. Studies have revealed that this bridging complex has multiple functions with structural roles in positioning the nucleus within the cell, conveying signals across the membrane and organizing chromatin in the 3D nuclear space with impact on gene transcription. We also provide an up-to-date survey in nuclear dynamics research achieved so far in the model plant Arabidopsis thaliana that highlights its potential impact on several key plant functions such as growth, seed maturation and germination, reproduction and response to biotic and abiotic stress. Finally, we bring evidences that most of the constituents of the LINC Complex and associated components are, with some specificities, conserved in monocot and dicot crop species and are displaying very similar functions to those described for Arabidopsis. This leads us to suggest that a better knowledge of this system and a better account of its potential applications will in the future enhance the resilience and productivity of crop plants.
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Affiliation(s)
- David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University , Oxford, UK
| | - Sarah Mermet
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France
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10
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Layat E, Bourcy M, Cotterell S, Zdzieszyńska J, Desset S, Duc C, Tatout C, Bailly C, Probst AV. The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination. Int J Mol Sci 2021; 22:ijms22084031. [PMID: 33919775 PMCID: PMC8070706 DOI: 10.3390/ijms22084031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022] Open
Abstract
Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3.3 are expressed in Arabidopsis dry seeds and that embryo chromatin is characterized by a low H3.1/H3.3 ratio. Loss of HISTONE REGULATOR A (HIRA), a histone chaperone responsible for H3.3 deposition, reduces cellular H3 levels and increases chromatin accessibility in dry seeds. These molecular differences are accompanied by increased seed dormancy in hira-1 mutant seeds. The loss of HIRA negatively affects seed germination even in the absence of HISTONE MONOUBIQUITINATION 1 or TRANSCRIPTION ELONGATION FACTOR II S, known to be required for seed dormancy. Finally, hira-1 mutant seeds show lower germination efficiency when aged under controlled deterioration conditions or when facing unfavorable environmental conditions such as high salinity. Altogether, our results reveal a dependency of dry seed chromatin organization on the replication-independent histone deposition pathway and show that HIRA contributes to modulating seed dormancy and vigor.
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Affiliation(s)
- Elodie Layat
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Marie Bourcy
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Sylviane Cotterell
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Julia Zdzieszyńska
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences–SGGW, 02-776 Warsaw, Poland;
| | - Sophie Desset
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Céline Duc
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
| | - Christophe Tatout
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Christophe Bailly
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Aline V. Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
- Correspondence:
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11
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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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12
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Le Goff S, Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I. The H3 histone chaperone NASP SIM3 escorts CenH3 in Arabidopsis. Plant J 2020; 101:71-86. [PMID: 31463991 DOI: 10.1111/tpj.14518] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Centromeres define the chromosomal position where kinetochores form to link the chromosome to microtubules during mitosis and meiosis. Centromere identity is determined by incorporation of a specific histone H3 variant termed CenH3. As for other histones, escort and deposition of CenH3 must be ensured by histone chaperones, which handle the non-nucleosomal CenH3 pool and replenish CenH3 chromatin in dividing cells. Here, we show that the Arabidopsis orthologue of the mammalian NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) and Schizosaccharomyces pombe histone chaperone Sim3 is a soluble nuclear protein that binds the histone variant CenH3 and affects its abundance at the centromeres. NASPSIM3 is co-expressed with Arabidopsis CenH3 in dividing cells and binds directly to both the N-terminal tail and the histone fold domain of non-nucleosomal CenH3. Reduced NASPSIM3 expression negatively affects CenH3 deposition, identifying NASPSIM3 as a CenH3 histone chaperone.
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Affiliation(s)
- Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Burcu Nur Keçeli
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78 371, Olomouc, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Elisabeth Roitinger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | | | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Danny Geelen
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
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13
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Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C. Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus 2019; 10:181-212. [PMID: 31362571 PMCID: PMC6682351 DOI: 10.1080/19491034.2019.1644592] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.
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Affiliation(s)
- Tao Dumur
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Susan Duncan
- Norwich Research Park, Earlham Institute, Norwich, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Dimiter Prodanov
- Environment, Health and Safety, Neuroscience Research Flanders, Leuven, Belgium
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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14
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Simon L, Rabanal FA, Dubos T, Oliver C, Lauber D, Poulet A, Vogt A, Mandlbauer A, Le Goff S, Sommer A, Duborjal H, Tatout C, Probst AV. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana. Nucleic Acids Res 2019. [PMID: 29518237 PMCID: PMC5887818 DOI: 10.1093/nar/gky163] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.
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Affiliation(s)
- Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Fernando A Rabanal
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tristan Dubos
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Damien Lauber
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Andreas Sommer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hervé Duborjal
- Plant Engineering Platform, BIOGEMMA, Route d'Ennezat Centre de Recherche de Chappes, 63720 Chappes, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
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15
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Benoit M, Simon L, Desset S, Duc C, Cotterell S, Poulet A, Le Goff S, Tatout C, Probst AV. Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. New Phytol 2019; 221:385-398. [PMID: 29897636 DOI: 10.1111/nph.15248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/23/2023]
Abstract
Developmental phase transitions are often characterized by changes in the chromatin landscape and heterochromatin reorganization. In Arabidopsis, clustering of repetitive heterochromatic loci into so-called chromocenters is an important determinant of chromosome organization in nuclear space. Here, we investigated the molecular mechanisms involved in chromocenter formation during the switch from a heterotrophic to a photosynthetically competent state during early seedling development. We characterized the spatial organization and chromatin features at centromeric and pericentromeric repeats and identified mutant contexts with impaired chromocenter formation. We find that clustering of repetitive DNA loci into chromocenters takes place in a precise temporal window and results in reinforced transcriptional repression. Although repetitive sequences are enriched in H3K9me2 and linker histone H1 before repeat clustering, chromocenter formation involves increasing enrichment in H3.1 as well as H2A.W histone variants, hallmarks of heterochromatin. These processes are severely affected in mutants impaired in replication-coupled histone assembly mediated by CHROMATIN ASSEMBLY FACTOR 1 (CAF-1). We further reveal that histone deposition by CAF-1 is required for efficient H3K9me2 enrichment at repetitive sequences during chromocenter formation. Taken together, we show that chromocenter assembly during post-germination development requires dynamic changes in nucleosome composition and histone post-translational modifications orchestrated by the replication-coupled H3.1 deposition machinery.
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Affiliation(s)
- Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
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16
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Abstract
The precise location of chromatin domains within the cell nucleus has seen growing recognition in the past decade as an additional mechanism of controlling gene expression in both plants and animals (Dekker et al., 2017). Consequently, international efforts are devoted to understanding the organising principle of this organelle in plants, and notably the nature and the role of functional compartments on gene expression (Graumann et al., 2013; Sotelo-Silveira et al., 2018). The European cooperation 'Impact of Nuclear Domains on Gene Expression and Plant Traits' (INDEPTH) brings together molecular cell biologists, plant physiologists, bioinformaticians, image analysts and computer scientists. They aim to address the question of how nuclear architecture, chromatin organisation and gene expression are connected in plants, particularly in relation to traits of interest such as biomass, reproduction and resistance to pathogens (https://www.brookes.ac.uk/indepth/). The kick-off meeting of the INDEPTH consortium took place in Clermont-Ferrand, France, on 12-14th March 2018, where more than 80 researchers set the agenda for the coming four years of research and collaboration.
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Affiliation(s)
- Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Aline V Probst
- Université Clermont Auvergne, CNRS, INSERM, laboratoire GReD, F-63000 Clermont-Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Basel-Zürich Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, laboratoire GReD, F-63000 Clermont-Ferrand, France
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17
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Voisin M, Vanrobays E, Tatout C. Investigation of Nuclear Periphery Protein Interactions in Plants Using the Membrane Yeast Two-Hybrid (MbY2H) System. Methods Mol Biol 2018; 1840:221-235. [PMID: 30141048 DOI: 10.1007/978-1-4939-8691-0_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identification of membrane protein interactomes is a key issue to better understand how these molecules carry out their functions. However, protein-protein interactions using conventional interaction assays are particularly challenging for integral membrane proteins, because of their hydrophobic nature. Here we describe the membrane yeast two-hybrid (MbY2H) system, a powerful tool for identifying the interactors of membrane and membrane-associated proteins.
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Affiliation(s)
- Maxime Voisin
- Université Clermont Auvergne, CNRS, INSERM, Laboratoire GReD, F-63000, Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- Université Clermont Auvergne, CNRS, INSERM, Laboratoire GReD, F-63000, Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, Laboratoire GReD, F-63000, Clermont-Ferrand, France.
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18
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Desset S, Poulet A, Tatout C. Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ. Methods Mol Biol 2018; 1675:615-632. [PMID: 29052214 DOI: 10.1007/978-1-4939-7318-7_33] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.
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Affiliation(s)
- Sophie Desset
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France
| | - Axel Poulet
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France.
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19
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Duc C, Benoit M, Détourné G, Simon L, Poulet A, Jung M, Veluchamy A, Latrasse D, Le Goff S, Cotterell S, Tatout C, Benhamed M, Probst AV. Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression. Plant Cell 2017; 29:1773-1793. [PMID: 28684426 PMCID: PMC5559740 DOI: 10.1105/tpc.16.00877] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 05/23/2023]
Abstract
Histones are essential components of the nucleosome, the major chromatin subunit that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability. In this study, we characterize the Arabidopsis thaliana Alpha Thalassemia-mental Retardation X-linked (ATRX) ortholog and show that ATRX is involved in histone H3 deposition. Arabidopsis ATRX mutant alleles are viable, but show developmental defects and reduced fertility. Their combination with mutants of the histone H3.3 chaperone HIRA (Histone Regulator A) results in impaired plant survival, suggesting that HIRA and ATRX function in complementary histone deposition pathways. Indeed, ATRX loss of function alters cellular histone H3.3 pools and in consequence modulates the H3.1/H3.3 balance in the cell. H3.3 levels are affected especially at genes characterized by elevated H3.3 occupancy, including the 45S ribosomal DNA (45S rDNA) loci, where loss of ATRX results in altered expression of specific 45S rDNA sequence variants. At the genome-wide scale, our data indicate that ATRX modifies gene expression concomitantly to H3.3 deposition at a set of genes characterized both by elevated H3.3 occupancy and high expression. Together, our results show that ATRX is involved in H3.3 deposition and emphasize the role of histone chaperones in adjusting genome expression.
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Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Gwénaëlle Détourné
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Matthieu Jung
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch, France
| | - Alaguraj Veluchamy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
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Poulet A, Duc C, Voisin M, Desset S, Tutois S, Vanrobays E, Benoit M, Evans DE, Probst AV, Tatout C. The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Sci 2017; 130:590-601. [PMID: 28049722 DOI: 10.1242/jcs.194712] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/04/2016] [Indexed: 12/20/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionarily well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its involvement in chromatin organisation has not been studied in plants. Here, 3D imaging methods have been used to investigate nuclear morphology and chromatin organisation in interphase nuclei of the model plant Arabidopsis thaliana in which heterochromatin clusters in conspicuous chromatin domains called chromocentres. Chromocentres form a repressive chromatin environment contributing to transcriptional silencing of repeated sequences, a general mechanism needed for genome stability. Quantitative measurements of the 3D position of chromocentres indicate their close proximity to the nuclear periphery but that their position varies with nuclear volume and can be altered in specific mutants affecting the LINC complex. Finally, we propose that the plant LINC complex contributes to proper heterochromatin organisation and positioning at the nuclear periphery, since its alteration is associated with the release of transcriptional silencing as well as decompaction of heterochromatic sequences.
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Affiliation(s)
- Axel Poulet
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France.,Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Céline Duc
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Maxime Voisin
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sophie Desset
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sylvie Tutois
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Matthias Benoit
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - David E Evans
- Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
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Poulet A, Probst AV, Graumann K, Tatout C, Evans D. Exploring the evolution of the proteins of the plant nuclear envelope. Nucleus 2017; 8:46-59. [PMID: 27644504 PMCID: PMC5287204 DOI: 10.1080/19491034.2016.1236166] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/22/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022] Open
Abstract
In this study, we explore the plasticity during evolution of proteins of the higher plant nuclear envelope (NE) from the most ancestral plant species to advanced angiosperms. The higher plant NE contains a functional Linker of Nucleoskeleton and Cytoskeleton (LINC) complex based on conserved Sad1-Unc84 (SUN) domain proteins and plant specific Klarsicht/Anc1/Syne homology (KASH) domain proteins. Recent evidence suggests the presence of a plant lamina underneath the inner membrane and various coiled-coil proteins have been hypothesized to be associated with it including Crowded Nuclei (CRWN; also termed LINC and NMCP), Nuclear Envelope Associated Protein (NEAP) protein families as well as the CRWN binding protein KAKU4. SUN domain proteins appear throughout with a key role for mid-SUN proteins suggested. Evolution of KASH domain proteins has resulted in increasing complexity, with some appearing in all species considered, while other KASH proteins are progressively gained during evolution. Failure to identify CRWN homologs in unicellular organisms included in the study and their presence in plants leads us to speculate that convergent evolution may have occurred in the formation of the lamina with each kingdom having new proteins such as the Lamin B receptor (LBR) and Lamin-Emerin-Man1 (LEM) domain proteins (animals) or NEAPs and KAKU4 (plants). Our data support a model in which increasing complexity at the nuclear envelope occurred through the plant lineage and suggest a key role for mid-SUN proteins as an early and essential component of the nuclear envelope.
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Affiliation(s)
- Axel Poulet
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - Aline V. Probst
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Christophe Tatout
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - David Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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Pawar V, Poulet A, Détourné G, Tatout C, Vanrobays E, Evans DE, Graumann K. A novel family of plant nuclear envelope-associated proteins. J Exp Bot 2016; 67:5699-5710. [PMID: 27630107 DOI: 10.1093/jxb/erw332] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This paper describes the characterisation of a new family of higher plant nuclear envelope-associated proteins (NEAPs) that interact with other proteins of the nuclear envelope. In the model plant Arabidopsis thaliana, the family consists of three genes expressed ubiquitously (AtNEAP1-3) and a pseudogene (AtNEAP4). NEAPs consist of extensive coiled-coil domains, followed by a nuclear localisation signal and a C-terminal predicted transmembrane domain. Domain deletion mutants confirm the presence of a functional nuclear localisation signal and transmembrane domain. AtNEAP proteins localise to the nuclear periphery as part of stable protein complexes, are able to form homo- and heteromers, and interact with the SUN domain proteins AtSUN1 and AtSUN2, involved in the linker of nucleoskeleton and cytoskeleton (LINC) complex. An A. thaliana cDNA library screen identified a putative transcription factor called AtbZIP18 as a novel interactor of AtNEAP1, which suggest a connection between NEAP and chromatin. An Atneap1 Atneap3 double-knockout mutant showed reduced root growth, and altered nuclear morphology and chromatin structure. Thus AtNEAPs are suggested as inner nuclear membrane-anchored coiled-coil proteins with roles in maintaining nuclear morphology and chromatin structure.
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Affiliation(s)
- Vidya Pawar
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, Avenue des Landais 63171 Aubière Cedex, France
| | - Axel Poulet
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, Avenue des Landais 63171 Aubière Cedex, France
| | - Gwénaëlle Détourné
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, Avenue des Landais 63171 Aubière Cedex, France
| | - Christophe Tatout
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, Avenue des Landais 63171 Aubière Cedex, France
| | - Emmanuel Vanrobays
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, Avenue des Landais 63171 Aubière Cedex, France
| | - David E Evans
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
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Abstract
In non-plant systems, chromatin association with the nuclear periphery affects gene expression, where interactions with nuclear envelope proteins can repress and interactions with nucleoporins can enhance transcription. In plants, both hetero- and euchromatin can localize at the nuclear periphery, but the effect of proximity to the nuclear periphery on gene expression remains largely unknown. This study explores the putative function of Seh1 and Nup50a nucleoporins on gene expression by using the Lac Operator / Lac Repressor (LacI-LacO) system adapted to Arabidopsis thaliana. We used LacO fused to the luciferase reporter gene (LacO:Luc) to investigate whether binding of the LacO:Luc transgene to nucleoporin:LacI protein fusions alters luciferase expression. Two separate nucleoporin-LacI-YFP fusions were introduced into single insert, homozygous LacO:Luc Arabidopsis plants. Homozygous plants carrying LacO:Luc and a single insert of either Seh1-LacI-YFP or Nup50a-LacI-YFP were tested for luciferase activity and compared to plants containing LacO:Luc only. Seh1-LacI-YFP increased, while Nup50a-LacI-YFP decreased luciferase activity. Seh1-LacI-YFP accumulated at the nuclear periphery as expected, while Nup50a-LacI-YFP was nucleoplasmic and was not selected for further study. Protein and RNA levels of luciferase were quantified by western blotting and RT-qPCR, respectively. Increased luciferase activity in LacO:Luc+Seh1-LacI-YFP plants was correlated with increased luciferase protein and RNA levels. This change of luciferase expression was abolished by disruption of LacI-LacO binding by treating with IPTG in young seedlings, rosette leaves and inflorescences. This study suggests that association with the nuclear periphery is involved in the regulation of gene expression in plants.
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Affiliation(s)
- Sarah Smith
- a Department of Biological and Medical Sciences ; Faculty of Health and Life Sciences; Oxford Brookes University ; Headington , Oxford , UK
| | - Carla Galinha
- a Department of Biological and Medical Sciences ; Faculty of Health and Life Sciences; Oxford Brookes University ; Headington , Oxford , UK
| | - Sophie Desset
- b UMR CNRS 6247; INSERM U931 GReD Clermont Universités 24 ; Aubiere , France
| | - Frances Tolmie
- a Department of Biological and Medical Sciences ; Faculty of Health and Life Sciences; Oxford Brookes University ; Headington , Oxford , UK
| | - David Evans
- a Department of Biological and Medical Sciences ; Faculty of Health and Life Sciences; Oxford Brookes University ; Headington , Oxford , UK
| | - Christophe Tatout
- b UMR CNRS 6247; INSERM U931 GReD Clermont Universités 24 ; Aubiere , France
| | - Katja Graumann
- a Department of Biological and Medical Sciences ; Faculty of Health and Life Sciences; Oxford Brookes University ; Headington , Oxford , UK
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24
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Simon L, Voisin M, Tatout C, Probst AV. Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana. Front Plant Sci 2015; 6:1049. [PMID: 26648952 PMCID: PMC4663263 DOI: 10.3389/fpls.2015.01049] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/09/2015] [Indexed: 05/23/2023]
Abstract
The centromere is a specific chromosomal region where the kinetochore assembles to ensure the faithful segregation of sister chromatids during mitosis and meiosis. Centromeres are defined by a local enrichment of the specific histone variant CenH3 mostly at repetitive satellite sequences. A larger pericentromeric region containing repetitive sequences and transposable elements surrounds the centromere that adopts a particular chromatin state characterized by specific histone variants and post-translational modifications and forms a transcriptionally repressive chromosomal environment. In the model organism Arabidopsis thaliana centromeric and pericentromeric domains form conspicuous heterochromatin clusters called chromocenters in interphase. Here we discuss, using Arabidopsis as example, recent insight into mechanisms involved in maintenance and establishment of centromeric and pericentromeric chromatin signatures as well as in chromocenter formation.
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Affiliation(s)
| | - Maxime Voisin
- †These authors have contributed equally to this work.
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Duc C, Benoit M, Le Goff S, Simon L, Poulet A, Cotterell S, Tatout C, Probst AV. The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants. Plant J 2015; 81:707-22. [PMID: 25600486 DOI: 10.1111/tpj.12758] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/21/2014] [Accepted: 12/23/2014] [Indexed: 05/09/2023]
Abstract
Chromatin organization is essential for coordinated gene expression, genome stability, and inheritance of epigenetic information. The main components involved in chromatin assembly are specific complexes such as Chromatin Assembly Factor 1 (CAF-1) and Histone Regulator (HIR), which deposit histones in a DNA synthesis-dependent or -independent manner, respectively. Here, we characterize the role of the plant orthologs Histone Regulator A (HIRA), Ubinuclein (UBN) and Calcineurin Binding protein 1 (CABIN1), which constitute the HIR complex. Arabidopsis loss-of-function mutants for the various subunits of the complex are viable, but hira mutants show reduced fertility. We show that loss of HIRA reduces extractable histone H3 protein levels and decreases nucleosome occupancy at both actively transcribed genes and heterochromatic regions. Concomitantly, HIRA contributes to maintenance of silencing of pericentromeric repeats and certain transposons. A genetic analysis based on crosses between mutants deficient in subunits of the CAF-1 and HIR complexes showed that simultaneous loss of both the CAF-1 and HIR histone H3 chaperone complexes severely affects plant survival, growth and reproductive development. Our results suggest that HIRA partially rescues impaired histone deposition in fas mutants to preserve nucleosome occupancy, implying plasticity in histone variant interaction and deposition.
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Affiliation(s)
- Céline Duc
- Génétique, Reproduction et Développement, CNRS UMR 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, Aubière Cedex, 63171, France
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26
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Abstract
Significant advances in understanding the plant nuclear envelope have been made over the past few years; indeed, knowledge of the protein network at the nuclear envelope is rapidly growing. One such network, the linker of nucleoskeleton and cytoskeleton (LINC) complex, is known in animals to connect chromatin to the cytoskeleton through the nuclear envelope. The LINC complex is made of Sad1/Unc84 (SUN) and Klarsicht/Anc1/Syne1 homology (KASH) proteins which have been recently characterized in plants. SUN proteins are located within the inner nuclear membrane, while the KASH proteins are included into the outer nuclear membrane. SUN and KASH domains interact and bridge the two nuclear membranes. In Arabidopsis, KASH proteins also interact with the tryptophan-proline-proline (WPP) domain-interacting tail-anchored protein 1 (WIT1), associated with the nuclear pore complex and with myosin XI-i which directly interacts with the actin cytoskeleton. Although evidence for a plant LINC complex connecting the nucleus to the cytoskeleton is growing, its interaction with chromatin is still unknown, but knowledge gained from animal models strongly suggests its existence in plants. Possible functions of the plant LINC complex in cell division, nuclear shape, and chromatin organization are discussed.
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Affiliation(s)
- Christophe Tatout
- Genetic reproduction and Development (GReD), UMR CNRS 6293 - Clermont Université - INSERM U 1103, 24 avenue des Landais, BP80026, 63171, Aubière CEDEX, France,
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Graumann K, Vanrobays E, Tutois S, Probst AV, Evans DE, Tatout C. Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK. J Exp Bot 2014; 65:6499-512. [PMID: 25217773 DOI: 10.1093/jxb/eru368] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
SUN-domain proteins belong to a gene family including classical Cter-SUN and mid-SUN subfamilies differentiated by the position of the SUN domain within the protein. Although present in animal and plant species, mid-SUN proteins have so far remained poorly described. Here, we used a combination of genetics, yeast two-hybrid and in planta transient expression methods to better characterize the SUN family in Arabidopsis thaliana. First, we validated the mid-SUN protein subfamily as a monophyletic group conserved from yeast to plant. Arabidopsis Cter-SUN (AtSUN1 and AtSUN2) and mid-SUN (AtSUN3 and AtSUN4) proteins expressed as fluorescent protein fusions are membrane-associated and localize to the nuclear envelope (NE) and endoplasmic reticulum. However, only the Cter-SUN subfamily is enriched at the NE. We investigated interactions in and between members of the two subfamilies and identified the coiled-coil domain as necessary for mediating interactions. The functional significance of the mid-SUN subfamily was further confirmed in mutant plants as essential for early seed development and involved in nuclear morphology. Finally, we demonstrated that both subfamilies interact with the KASH domain of AtWIP1 and identified a new root-specific KASH-domain protein, AtTIK. AtTIK localizes to the NE and affects nuclear morphology. Our study indicates that Arabidopsis Cter-SUN and mid-SUN proteins are involved in a complex protein network at the nuclear membranes, reminiscent of the LInker of Nucleoskeleton and Cytoskeleton (LINC) complex found in other kingdoms.
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Affiliation(s)
- Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Emmanuel Vanrobays
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, 24 Avenue des Landais, BP80026 63171 Aubière Cedex, France
| | - Sylvie Tutois
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, 24 Avenue des Landais, BP80026 63171 Aubière Cedex, France
| | - Aline V Probst
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, 24 Avenue des Landais, BP80026 63171 Aubière Cedex, France
| | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christophe Tatout
- UMR CNRS 6293 INSERM U 1103 Clermont Université, GReD, 24 Avenue des Landais, BP80026 63171 Aubière Cedex, France
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28
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Poulet A, Arganda-Carreras I, Legland D, Probst AV, Andrey P, Tatout C. NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics 2014; 31:1144-6. [DOI: 10.1093/bioinformatics/btu774] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/14/2014] [Indexed: 11/12/2022] Open
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29
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Thomas M, Pingault L, Poulet A, Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV, Tatout C. Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics 2014; 15:922. [PMID: 25342325 PMCID: PMC4223845 DOI: 10.1186/1471-2164-15-922] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in the hexaploid wheat Triticum aestivum (TaMET1). RESULTS Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7, indicating that group 2 homoeologous genes are predominant at the transcriptional level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous group 5 and 7, but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1. CONCLUSIONS We retraced the evolutionary history of MET1 genes in wheat, explaining the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
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Affiliation(s)
- Mélanie Thomas
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Lise Pingault
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Axel Poulet
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Jorge Duarte
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Mickaël Throude
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Sébastien Faure
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Jean-Philippe Pichon
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Etienne Paux
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Aline Valeska Probst
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Christophe Tatout
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
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Docouier M, Gauthier E, Tatout C, Pinon H. Controlling and addressing a retrotransposon in the Drosophila egg chamber. Biol Cell 2012. [DOI: 10.1016/0248-4900(96)81343-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tamasloukht B, Wong Quai Lam MSJ, Martinez Y, Tozo K, Barbier O, Jourda C, Jauneau A, Borderies G, Balzergue S, Renou JP, Huguet S, Martinant JP, Tatout C, Lapierre C, Barrière Y, Goffner D, Pichon M. Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression. J Exp Bot 2011; 62:3837-48. [PMID: 21493812 PMCID: PMC3134344 DOI: 10.1093/jxb/err077] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cinnamoyl-CoA reductase (CCR), which catalyses the first committed step of the lignin-specific branch of monolignol biosynthesis, has been extensively characterized in dicot species, but few data are available in monocots. By screening a Mu insertional mutant collection in maize, a mutant in the CCR1 gene was isolated named Zmccr1(-). In this mutant, CCR1 gene expression is reduced to 31% of the residual wild-type level. Zmccr1(-) exhibited enhanced digestibility without compromising plant growth and development. Lignin analysis revealed a slight decrease in lignin content and significant changes in lignin structure. p-Hydroxyphenyl units were strongly decreased and the syringyl/guaiacyl ratio was slightly increased. At the cellular level, alterations in lignin deposition were mainly observed in the walls of the sclerenchymatic fibre cells surrounding the vascular bundles. These cell walls showed little to no staining with phloroglucinol. These histochemical changes were accompanied by an increase in sclerenchyma surface area and an alteration in cell shape. In keeping with this cell type-specific phenotype, transcriptomics performed at an early stage of plant development revealed the down-regulation of genes specifically associated with fibre wall formation. To the present authors' knowledge, this is the first functional characterization of CCR1 in a grass species.
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Affiliation(s)
- Barek Tamasloukht
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Mary Sarah-Jane Wong Quai Lam
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Yves Martinez
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Koffi Tozo
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Odile Barbier
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Cyril Jourda
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Alain Jauneau
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Gisèle Borderies
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Sandrine Balzergue
- INRA/CNRS - URGV 2, rue Gaston Crémieux, CP5708, 91057 Evry cedex, France
| | - Jean-Pierre Renou
- INRA/CNRS - URGV 2, rue Gaston Crémieux, CP5708, 91057 Evry cedex, France
| | - Stéphanie Huguet
- INRA/CNRS - URGV 2, rue Gaston Crémieux, CP5708, 91057 Evry cedex, France
| | - Jean Pierre Martinant
- Biogemma, Campus universitaire des Cézeaux, 24 Avenue des Landais, 63170 Aubière, France
| | - Christophe Tatout
- Biogemma, Campus universitaire des Cézeaux, 24 Avenue des Landais, 63170 Aubière, France
| | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, UMR 1318 AgroParisTech/INRA, F-78026 Versailles Cedex, France
| | - Yves Barrière
- INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, BP6, 86600 Lusignan, France
| | - Deborah Goffner
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
| | - Magalie Pichon
- Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Pôle de Biotechnologies Végétales,24 chemin de Borde Rouge, B.P. 42617 Auzeville, 31326 Castanet Tolosan, France
- To whom correspondence should be addressed. E-mail:
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Gutiérrez-Marcos JF, Dal Prà M, Giulini A, Costa LM, Gavazzi G, Cordelier S, Sellam O, Tatout C, Paul W, Perez P, Dickinson HG, Consonni G. empty pericarp4 encodes a mitochondrion-targeted pentatricopeptide repeat protein necessary for seed development and plant growth in maize. Plant Cell 2007; 19:196-210. [PMID: 17259266 PMCID: PMC1820960 DOI: 10.1105/tpc.105.039594] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The pentatricopeptide repeat (PPR) family represents one of the largest gene families in plants, with >440 members annotated in Arabidopsis thaliana. PPR proteins are thought to have a major role in the regulation of posttranscriptional processes in organelles. Recent studies have shown that Arabidopsis PPR proteins play an essential, nonredundant role during embryogenesis. Here, we demonstrate that mutations in empty pericarp4 (emp4), a maize (Zea mays) PPR-encoding gene, confer a seed-lethal phenotype. Mutant endosperms are severely impaired, with highly irregular differentiation of transfer cells in the nutrient-importing basal endosperm. Analysis of homozygous mutant plants generated from embryo-rescue experiments indicated that emp4 also affects general plant growth. The emp4-1 mutation was identified in an active Mutator (Mu) population, and cosegregation analysis revealed that it arose from a Mu3 element insertion. Evidence of emp4 molecular cloning was provided by the isolation of four additional emp4 alleles obtained by a reverse genetics approach. emp4 encodes a novel type of PPR protein of 614 amino acids. EMP4 contains nine 35-amino acid PPR motifs and an N-terminal mitochondrion-targeted sequence peptide, which was confirmed by a translational EMP4-green fluorescent protein fusion that localized to mitochondria. Molecular analyses further suggest that EMP4 is necessary to regulate the correct expression of a small subset of mitochondrial transcripts in the endosperm.
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Martin A, Lee J, Kichey T, Gerentes D, Zivy M, Tatout C, Dubois F, Balliau T, Valot B, Davanture M, Tercé-Laforgue T, Quilleré I, Coque M, Gallais A, Gonzalez-Moro MB, Bethencourt L, Habash DZ, Lea PJ, Charcosset A, Perez P, Murigneux A, Sakakibara H, Edwards KJ, Hirel B. Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell 2006; 18:3252-74. [PMID: 17138698 PMCID: PMC1693956 DOI: 10.1105/tpc.106.042689] [Citation(s) in RCA: 279] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The roles of two cytosolic maize glutamine synthetase isoenzymes (GS1), products of the Gln1-3 and Gln1-4 genes, were investigated by examining the impact of knockout mutations on kernel yield. In the gln1-3 and gln1-4 single mutants and the gln1-3 gln1-4 double mutant, GS mRNA expression was impaired, resulting in reduced GS1 protein and activity. The gln1-4 phenotype displayed reduced kernel size and gln1-3 reduced kernel number, with both phenotypes displayed in gln1-3 gln1-4. However, at maturity, shoot biomass production was not modified in either the single mutants or double mutants, suggesting a specific impact on grain production in both mutants. Asn increased in the leaves of the mutants during grain filling, indicating that it probably accumulates to circumvent ammonium buildup resulting from lower GS1 activity. Phloem sap analysis revealed that unlike Gln, Asn is not efficiently transported to developing kernels, apparently causing reduced kernel production. When Gln1-3 was overexpressed constitutively in leaves, kernel number increased by 30%, providing further evidence that GS1-3 plays a major role in kernel yield. Cytoimmunochemistry and in situ hybridization revealed that GS1-3 is present in mesophyll cells, whereas GS1-4 is specifically localized in the bundle sheath cells. The two GS1 isoenzymes play nonredundant roles with respect to their tissue-specific localization.
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Affiliation(s)
- Antoine Martin
- Unité de Nutrition Azotée des Plantes UR511, Institut National de la Recherche Agronomique, F-78026 Versailles Cedex, France
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Kärkönen A, Murigneux A, Martinant JP, Pepey E, Tatout C, Dudley B, Fry S. UDP-glucose dehydrogenases of maize: a role in cell wall pentose biosynthesis. Biochem J 2006; 391:409-15. [PMID: 15969652 PMCID: PMC1276940 DOI: 10.1042/bj20050800] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
UDPGDH (UDP-D-glucose dehydrogenase) oxidizes UDP-Glc (UDP-D-glucose) to UDP-GlcA (UDP-D-glucuronate), the precursor of UDP-D-xylose and UDP-L-arabinose, major cell wall polysaccharide precursors. Maize (Zea mays L.) has at least two putative UDPGDH genes (A and B), according to sequence similarity to a soya bean UDPGDH gene. The predicted maize amino acid sequences have 95% similarity to that of soya bean. Maize mutants with a Mu-element insertion in UDPGDH-A or UDPGDH-B were isolated (udpgdh-A1 and udpgdh-B1 respectively) and studied for changes in wall polysaccharide biosynthesis. The udpgdh-A1 and udpgdh-B1 homozygotes showed no visible phenotype but exhibited 90 and 60-70% less UDPGDH activity respectively than wild-types in a radiochemical assay with 30 microM UDP-glucose. Ethanol dehydrogenase (ADH) activity varied independently of UDPGDH activity, supporting the hypothesis that ADH and UDPGDH activities are due to different enzymes in maize. When extracts from wild-types and udpgdh-A1 homozygotes were assayed with increasing concentrations of UDP-Glc, at least two isoforms of UDPGDH were detected, having K(m) values of approx. 380 and 950 microM for UDP-Glc. Leaf and stem non-cellulosic polysaccharides had lower Ara/Gal and Xyl/Gal ratios in udpgdh-A1 homozygotes than in wild-types, whereas udpgdh-B1 homozygotes exhibited more variability among individual plants, suggesting that UDPGDH-A activity has a more important role than UDPGDH-B in UDP-GlcA synthesis. The fact that mutation of a UDPGDH gene interferes with polysaccharide synthesis suggests a greater importance for the sugar nucleotide oxidation pathway than for the myo-inositol pathway in UDP-GlcA biosynthesis during post-germinative growth of maize.
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Affiliation(s)
- Anna Kärkönen
- *The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Edinburgh EH9 3JH, U.K
| | - Alain Murigneux
- †BIOGEMMA, Campus Universitaire des Cézeaux, 24, Avenue des Landais, 63170 Aubière, France
| | - Jean-Pierre Martinant
- †BIOGEMMA, Campus Universitaire des Cézeaux, 24, Avenue des Landais, 63170 Aubière, France
| | - Elodie Pepey
- †BIOGEMMA, Campus Universitaire des Cézeaux, 24, Avenue des Landais, 63170 Aubière, France
| | - Christophe Tatout
- †BIOGEMMA, Campus Universitaire des Cézeaux, 24, Avenue des Landais, 63170 Aubière, France
| | - Bernard J. Dudley
- *The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Edinburgh EH9 3JH, U.K
| | - Stephen C. Fry
- *The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Edinburgh EH9 3JH, U.K
- To whom correspondence should be addressed (email )
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Pélissier T, Tatout C, Lavige JM, Busseau I, Bucheton A, Deragon JM. Utilization of the IR hybrid dysgenesis system in Drosophila to test in vivo mobilization of synthetic SINEs sharing 3' homology with the I factor. Gene 2002; 285:239-45. [PMID: 12039051 DOI: 10.1016/s0378-1119(02)00400-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The current model of short interspersed nuclear element (SINE) mobility suggests that these non-coding retroposons are able to recruit for their own benefits the enzymatic machinery encoded by autonomous long interspersed nuclear elements (LINEs). The recent characterization of potential SINE-LINE partner pairs that share common 3' end sequences concurs with this model and has led to a potent picture of tRNA-derived SINEs consisting of a tripartite functional structure (Mol. Cell. Biol. 16 (1996) 3756; Mol. Biol. Evol. 16 (1999) 1238; Proc. Natl. Acad. Sci. USA 96 (1999) 2869). This structure consist of a 5' polIII tRNA-related promoter region, a central conserved domain and a variable 3' region with homology to the 3' end of LINEs, believed to be essential to direct recognition by the LINE proteins. To test this model in vivo, we have designed synthetic SINEs possessing this 'canonical' structure, including 3' homology to the 3' UTR of the LINE I factor from Drosophila. These synthetic elements were introduced in a Drosophila reactive strain, and SINE retroposition was assessed following dysgenic crosses that are known to induce high levels of I factor germinal transposition. In the progeny from the dysgenic crosses 3400-4000 flies were analyzed but no retroposed copy of the chimeric SINEs was detected, indicating that what is assumed to be a typical SINE structure is not sufficient per se to allow efficient trans-mobilization of our synthetic SINEs by an actively amplifying partner LINE. Alternatively, the apparent absence of natural fly SINEs may underline intrinsic properties of fly biology that are incompatible with the genesis and/or propagation of SINE-like elements.
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Affiliation(s)
- Thierry Pélissier
- CNRS UMR 6547 and GDR 2157, Biomove, Université Blaise Pascal, 24 Avenue des Landais, 63177 Cedex, Aubière, France.
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Tikhonov AP, Lavie L, Tatout C, Bennetzen JL, Avramova Z, Deragon JM. Target sites for SINE integration in Brassica genomes display nuclear matrix binding activity. Chromosome Res 2002; 9:325-37. [PMID: 11419796 DOI: 10.1023/a:1016650830798] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Short interspersed nuclear elements (SINEs) are ubiquitous components of complex animal and plant genomes. SINEs are believed to be important players in eukaryotic genome evolution. Studies on SINE integration sites have revealed non-random integration without strict nucleotide sequence requirements for the integration target, suggesting that the targeted DNA might assume specific secondary structures or protein associations. Here, we report that S1 SINE elements in the genomes of Brassica show an interesting preference for matrix attachment regions (MARs). Ten cloned genomic regions were tested for their ability to bind the nuclear matrix both before and after a SINE integration event. Eight of the genomic regions targeted by S1 display strong affinity for the nuclear matrix, while two show weaker binding. The SINE S1 did not display any matrix-binding capacity on its own in either non-methylated or methylated forms. In vivo, an integrated S1 is methylated while the surrounding genomic regions may remain undermethylated or undergo methylation. However, tested genomic regions containing methylated S1, with or without methylated flanking genomic sequences, were found to vary in their ability to bind the matrix in vitro. These results suggest a possible molecular basis for a preferential targeting of SINEs to MARs and a possible impact of the integration events upon gene and genome function.
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Affiliation(s)
- A P Tikhonov
- Department of Biology, Purdue University, West Lafayette, IN 47907, USA
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Tatout C, Gauthier E, Pinon H. Rapid evaluation in
Escherichia coli of
antisense RNAs and ribozymes. Lett Appl Microbiol 2002. [DOI: 10.1046/j.1472-765x.1998.t01-2-00449.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- C. Tatout
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard, Villeurbanne Cedex, France
| | - E. Gauthier
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard, Villeurbanne Cedex, France
| | - H. Pinon
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard, Villeurbanne Cedex, France
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Dellino GI, Tatout C, Pirrotta V. Extensive conservation of sequences and chromatin structures in the bxd polycomb response element among Drosophilid species. Int J Dev Biol 2002; 46:133-41. [PMID: 11902674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The Polycomb Response Element (PRE) is the nucleation site for the Polycomb silencing complexes. The sequences responsible for the recruitment of the components of the Polycomb complex are not well understood. A comparison of the bxd PRE sequences from several different Drosophila species shows that some changes have occurred during phylogeny but large blocks of sequence are conserved after a divergence of some 60 million years. We compare the PRE sequences, the sites of some known PRE binding proteins, the conservation of DNasel hypersensitive sites and relate them to the sequence of the Ultrabithorax promoter which these PREs regulate.
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Abstract
The I factor (IF) is a LINE-like transposable element from Drosophila melanogaster. IF is silenced in most strains, but under special circumstances its transposition can be induced and correlates with the appearance of a syndrome of female sterility called hybrid dysgenesis. To elucidate the relationship between IF expression and female sterility, different transgenic antisense and/or sense RNAs homologous to the IF ORF1 have been expressed. Increasing the transgene copy number decreases both the expression of an IF-lacZ fusion and the intensity of the female sterile phenotype, demonstrating that IF expression is correlated with sterility. Some transgenes, however, exert their repressive abilities not only through a copy number-dependent zygotic effect, but also through additional maternal and paternal effects that may be induced at the DNA and/or RNA level. Properties of the maternal effect have been detailed: (1) it represses hybrid dysgenesis more efficiently than does the paternal effect; (2) its efficacy increases with both the transgene copy number and the aging of sterile females; (3) it accumulates slowly over generations after the transgene has been established; and (4) it is maintained for at least two generations after transgene removal. Conversely, the paternal effect increases only with female aging. The last two properties of the maternal effect and the genuine existence of a paternal effect argue for the occurrence, in the IF regulation pathway, of a cellular memory transmitted through mitosis, as well as through male and female meiosis, and akin to epigenetic phenomena.
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Affiliation(s)
- E Gauthier
- Centre de Génétique Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard, F-69622 Villeurbanne Cedex, France
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Horard B, Tatout C, Poux S, Pirrotta V. Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol Cell Biol 2000; 20:3187-97. [PMID: 10757803 PMCID: PMC85613 DOI: 10.1128/mcb.20.9.3187-3197.2000] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polycomb response elements (PREs) are regulatory sites that mediate the silencing of homeotic and other genes. The bxd PRE region from the Drosophila Ultrabithorax gene can be subdivided into subfragments of 100 to 200 bp that retain different degrees of PRE activity in vivo. In vitro, embryonic nuclear extracts form complexes containing Polycomb group (PcG) proteins with these fragments. PcG binding to some fragments is dependent on consensus sequences for the GAGA factor. Other fragments lack GAGA binding sites but can still bind PcG complexes in vitro. We show that the GAGA factor is a component of at least some types of PcG complexes and may participate in the assembly of PcG complexes at PREs.
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Affiliation(s)
- B Horard
- Department of Zoology, University of Geneva, CH1211 Geneva, Switzerland
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Delattre M, Tatout C, Coen D. P-element transposition in Drosophila melanogaster: influence of size and arrangement in pairs. Mol Gen Genet 2000; 263:445-54. [PMID: 10821178 DOI: 10.1007/pl00008684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Drosophila melanogaster, several factors have been suggested to influence the rates of P-element transposition and excision, including position effects, size and structure of the elements and differences in transposase source. We have investigated the effect of the size of the starting P-element on the rates of excision and transposition. Four transgenes localized at the same insertion site on the X chromosome and which differ by the number of copies of an internal repeated sequence, were studied. Transgenes with sizes ranging from 11 kb to 22 kb excise at similar rates, and size does not correlate with the differences in transposition rate between them. We also studied the behavior of double P-elements, located at the same site and arranged in various configurations: nested, contiguous or separated by a few base pairs, in the same or reverse orientation. These double P-elements display different mobilities depending on the arrangement of the two transgenes. Transposition and excision rates were also studied for an insertion bearing four transgenes in very close proximity. Our results suggest that several neighboring elements could excise together. We also propose a new model to explain the formation of all the double P-elements we describe.
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Affiliation(s)
- M Delattre
- Département Dynamique du Génome et Evolution, Institut Jacques Monod, Paris, France.
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Goubely C, Arnaud P, Tatout C, Heslop-Harrison JS, Deragon JM. S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation. Plant Mol Biol 1999; 39:243-255. [PMID: 10080692 DOI: 10.1023/a:1006108325504] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA methylation has been often proposed to operate as a genome defence system against parasitic mobile elements. To test this possibility, the methylation status of a class of plant mobile elements, the S1Bn SINEs, was analysed in detail using the bisulfite modification method. We observed that S1Bn SINE retroposons are methylated at symmetrical and asymmetrical positions. Methylated cytosines are not limited to transcriptionally important regions but are well distributed along the sequence. S1Bn SINE retroposons are two-fold more methylated than the average methylation level of the Brassica napus nuclear DNA. By in situ hybridization, we showed that this high level of methylation does not result from the association of S1Bn elements to genomic regions known to be highly methylated suggesting that S1Bn elements were specifically methylated. A detailed analysis of the methylation context showed that S1Bn cytosines in symmetrical CpG and CpNpG sites are methylated at a level of 87% and 44% respectively. We observed that 5.3% of S1Bn cytosines in non-symmetrical positions were also methylated. Of this asymmetrical methylation, 57% occurred at a precise motif (Cp(A/T)pA) that only represented 12% of the asymmetrical sites in S1Bn sequences suggesting that it represents a preferred asymmetrical methylation site. This motif is methylated in S1Bn elements at only half the level observed for the Cp(A/T)pG sites. We show that non-S1Bn CpTpA sites can also be methylated in DNA from B. napus and from other plant species.
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Affiliation(s)
- C Goubely
- Department of Cell Biology, John Innes Centre, Norwich, UK
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Tatout C, Gauthier E, Pinon H. Rapid evaluation in Escherichia coli of antisense RNAs and ribozymes. Lett Appl Microbiol 1998; 27:297-301. [PMID: 9830149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The characterization of a simple bacterial system using commercially available plasmids and strains, developed to assess the effectiveness of trans-acting (antisense RNA and ribozymes) RNA in Escherichia coli, is reported. This system was used to test various trans-acting RNA molecules against the expression of the I factor, a functional transposable element from Drosophila melanogaster. For this target, results indicate that antisense RNA efficiency depends on the hybridization length between sense and antisense RNA. The introduction of a single hammerhead ribozyme within the antisense RNAs does not increase its inhibitory activity. These predictions were subsequently confirmed in Drosophila melanogaster.
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Affiliation(s)
- C Tatout
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard, Villeurbanne, France
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Abstract
The reverse transcription of RNA in DNA is responsible for the generation of large families of repetitive sequences called retroposons or non-LTR retrotransposons. Recent reports established that the integration of mammalian SINE and LINE retroposons occurs at nonrandom staggered breaks, probably resulting from the action of a LINE-encoded endonuclease (Feng et al. 1996; Jurka 1997; Jurka et al. 1998). We report here that plant SINE S1 retroposons also integrate at nonrandom staggered breaks. One of the two nicks involved in S1 integration is associated mainly with the 5'-Y/AAANNNG-3' motif. The other nick at opposite DNA strand occurs preferably within 14-16 bp, a situation also observed for mammalian retroposons, but is not associated with any specific motif. Further studies on the distribution of dinucleotides surrounding the two nicking sites showed that, as for mammalian retroposons, S1 retroposons integrate at sites rich in TA, CA, and TG dinucleotides. These dinucleotides were reported as specific DNA sites where special DNA structures called "kinks" may occur under bending constraints. Nicking sites are preceded by peaks in frequency of di-pyrimidine followed by peaks of di-purine. These results suggest that the general A/T richness of a given DNA region and the presence of short runs of pyrimidines followed by short runs of purines could represent a favorable context for the integration of retroposons. In such a context, an endonuclease upon fixation could be able to generate the kink at the pyrimidine/purine transition and to nick the DNA. The similarities in target site selection observed for plant and mammalian retroposons suggest that retroposition is a surprisingly well conserved process.
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Affiliation(s)
- C Tatout
- Biomove, UMR6547 CNRS, Université Blaise Pascal Clermont-Ferrand II, 63177 Aubière Cedex, France
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Tatout C, Docquier M, Lachaume P, Mesure M, Lécher P, Pinon H. Germ-line expression of a functional LINE from Drosophila melanogaster: fine characterization allows for potential investigations of trans-regulators. Int J Dev Biol 1994; 38:27-33. [PMID: 8074994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The I factor (IF) is a functional non-viral retrotransposon, or LINE, from Drosophila melanogaster. It is mobilized in the germ-line of dysgenic SF females during I-R hybrid dysgenesis. In previous papers (Lachaume et al., Development 115: 729-735, 1992; Lachaume and Pinon, Mol. Gen. Gen. 240: 277-285, 1993) we used a transgenic fusion between the 5' part of the IF and the lacZ gene to characterize IF expression and its regulation. This I-lacZ transgenic fusion expresses beta-galactosidase activity during oogenesis. We established a Drosophila line bearing four transgenic insertions (the 4I-lacZ line) and got new insights about IF expression: (1) I-lacZ expression is proportional to the copy number of transgenes present in the genome, (2) the expression occurs just before or when meiosis begins, (3) this expression seems to be subjected to a variegation effect within the germ-line cells, (4) the transgenic activity is mainly directed toward the decondensed chromatin of nurse cells. The close relationship between I factor expression and oogenesis led us to investigate the role played by genes expressed during oogenesis on I factor expression. We present recent data indicating that mutants which interfere with oogenesis can also affect I factor expression. From this data we propose an original screen using the 41-lacZline to detect identified mutations which also affect I factor expression.
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Affiliation(s)
- C Tatout
- Laboratoire de Génétique, Université Blaise Pascal, Aubière, France
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