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Iwakawa H, Takahashi H, Machida Y, Machida C. Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial-Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis. Int J Mol Sci 2020; 21:E7314. [PMID: 33022996 PMCID: PMC7582388 DOI: 10.3390/ijms21197314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal-distal, adaxial-abaxial, and medial-lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial-abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.
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Affiliation(s)
- Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan;
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
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2
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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3
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Pontvianne F, Grob S. Three-dimensional nuclear organization in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2020; 133:479-488. [PMID: 32240449 DOI: 10.1007/s10265-020-01185-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/19/2020] [Indexed: 05/22/2023]
Abstract
In recent years, the study of plant three-dimensional nuclear architecture received increasing attention. Enabled by technological advances, our knowledge on nuclear architecture has greatly increased and we can now access large data sets describing its manifold aspects. The principles of nuclear organization in plants do not significantly differ from those in animals. Plant nuclear organization comprises various scales, ranging from gene loops to topologically associating domains to nuclear compartmentalization. However, whether plant three-dimensional chromosomal features also exert similar functions as in animals is less clear. This review discusses recent advances in the fields of three-dimensional chromosome folding and nuclear compartmentalization and describes a novel silencing mechanism, which is closely linked to nuclear architecture.
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Affiliation(s)
- Frédéric Pontvianne
- UPVD, LGDP, UMR5096, Université de Perpignan, Perpignan, France.
- CNRS, LGDP, UMR5096, Université de Perpignan, Perpignan, France.
| | - Stefan Grob
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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4
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Picart-Picolo A, Picart C, Picault N, Pontvianne F. Nucleolus-associated chromatin domains are maintained under heat stress, despite nucleolar reorganization in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2020; 133:463-470. [PMID: 32372397 DOI: 10.1007/s10265-020-01201-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/17/2020] [Indexed: 05/23/2023]
Abstract
Several layers of mechanisms participate in plant adaptation to heat-stress. For example, the plant metabolism switches from cell growth mode to stress adaptation mode. Ribosome biogenesis is one of the most energy costly pathways. That biogenesis process occurs in the nucleolus, the largest nuclear compartment, whose structure is highly dependent on this pathway. We used a nucleolar marker to track the structure of the nucleolus, and revealed a change in its sub-nucleolar distribution under heat stress. In addition, the nucleolus is implicated in other cellular processes, such as genome organization within the nucleus. However, our analyses of nucleolus-associated chromatin domains under heat stress did not reveal significant differences compared to the control plants, suggesting a lack of connection between two of the main functions of the nucleolus: ribosome biogenesis and nuclear organization.
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Affiliation(s)
- Ariadna Picart-Picolo
- CNRS, LGDP UMR5096, Université de Perpignan, Perpignan, France
- UPVD, LGDP UMR5096, Université de Perpignan, Perpignan, France
| | - Claire Picart
- CNRS, LGDP UMR5096, Université de Perpignan, Perpignan, France
- UPVD, LGDP UMR5096, Université de Perpignan, Perpignan, France
| | - Nathalie Picault
- CNRS, LGDP UMR5096, Université de Perpignan, Perpignan, France
- UPVD, LGDP UMR5096, Université de Perpignan, Perpignan, France
| | - Frederic Pontvianne
- CNRS, LGDP UMR5096, Université de Perpignan, Perpignan, France.
- UPVD, LGDP UMR5096, Université de Perpignan, Perpignan, France.
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5
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Pontvianne F, Liu C. Chromatin domains in space and their functional implications. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:1-10. [PMID: 31881292 DOI: 10.1016/j.pbi.2019.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 05/19/2023]
Abstract
Genome organization displays functional compartmentalization. Many factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs, shape chromatin domains and the three-dimensional genome organization. Various types of chromatin domains with distinct epigenetic and spatial features exhibit different transcriptional activities. As part of the efforts to better understand plant functional genomics, over the past a few years, spatial distribution patterns of plant chromatin domains have been brought to light. In this review, we discuss chromatin domains associated with the nuclear periphery and the nucleolus, as well as chromatin domains staying in proximity and showing physical interactions. The functional implication of these domains is discussed, with a particular focus on the transcriptional regulation and replication timing. Finally, from a biophysical point of view, we discuss potential roles of liquid-liquid phase separation in plant nuclei in the genesis and maintenance of spatial chromatin domains.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France; UPVD, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France.
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany.
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Báez M, Souza G, Guerra M. Does the chromosomal position of 35S rDNA sites influence their transcription? A survey on Nothoscordum species (Amaryllidaceae). Genet Mol Biol 2020; 43:e20180194. [PMID: 31469154 PMCID: PMC7197985 DOI: 10.1590/1678-4685-gmb-2018-0194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/21/2019] [Indexed: 11/22/2022] Open
Abstract
35S ribosomal DNA (rDNA) sites are the regions where the ribosomal genes 18S, 5.8S and 25S, responsible for the formation of the nucleoli, are found. The fact that rDNA sites have non-random distribution on chromosomes suggests that their positions may influence their transcription. To identify if the preferentially transcribed rDNA sites occupy specific position, six species (nine cytotypes) of the genus Nothoscordum were analyzed using two different techniques to impregnate the nucleolar organizer regions (NORs) with silver nitrate. Both techniques strongly stained NORs, but one of them also stained the proximal region of all chromosomes, suggesting the existence of another group of argentophilic proteins in this region. In species with rDNA sites in acrocentric and metacentric chromosomes, sites located on the short arms of the acrocentric chromosomes were preferentially activated. On the other hand, in species with rDNA sites restricted to the short arms of the acrocentrics, all of them were activated, whereas in those species with sites restricted to the terminal region of metacentric chromosomes, the frequency of active sites was always lower than expected. This indicate that, at least in Nothoscordum, the transcription of an rDNA site is influenced by its chromosomal position, and may explain, at least partially, the strongly non-random distribution of these sites in plant and animal chromosomes.
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Affiliation(s)
- Mariana Báez
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
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7
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Luo L, Ando S, Sakamoto Y, Suzuki T, Takahashi H, Ishibashi N, Kojima S, Kurihara D, Higashiyama T, Yamamoto KT, Matsunaga S, Machida C, Sasabe M, Machida Y. The formation of perinucleolar bodies is important for normal leaf development and requires the zinc-finger DNA-binding motif in Arabidopsis ASYMMETRIC LEAVES2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1118-1134. [PMID: 31639235 PMCID: PMC7155070 DOI: 10.1111/tpj.14579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 05/27/2023]
Abstract
In Arabidopsis, the ASYMMETRIC LEAVES2 (AS2) protein plays a key role in the formation of flat symmetric leaves via direct repression of the abaxial gene ETT/ARF3. AS2 encodes a plant-specific nuclear protein that contains the AS2/LOB domain, which includes a zinc-finger (ZF) motif that is conserved in the AS2/LOB family. We have shown that AS2 binds to the coding DNA of ETT/ARF3, which requires the ZF motif. AS2 is co-localized with AS1 in perinucleolar bodies (AS2 bodies). To identify the amino acid signals in AS2 required for formation of AS2 bodies and function(s) in leaf formation, we constructed recombinant DNAs that encoded mutant AS2 proteins fused to yellow fluorescent protein. We examined the subcellular localization of these proteins in cells of cotyledons and leaf primordia of transgenic plants and cultured cells. The amino acid signals essential for formation of AS2 bodies were located within and adjacent to the ZF motif. Mutant AS2 that failed to form AS2 bodies also failed to rescue the as2-1 mutation. Our results suggest the importance of the formation of AS2 bodies and the nature of interactions of AS2 with its target DNA and nucleolar factors including NUCLEOLIN1. The partial overlap of AS2 bodies with perinucleolar chromocenters with condensed ribosomal RNA genes implies a correlation between AS2 bodies and the chromatin state. Patterns of AS2 bodies in cells during interphase and mitosis in leaf primordia were distinct from those in cultured cells, suggesting that the formation and distribution of AS2 bodies are developmentally modulated in plants.
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Affiliation(s)
- Lilan Luo
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Present address:
Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Sayuri Ando
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Yuki Sakamoto
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
- Department of Biological SciencesGraduate School of ScienceOsaka University1‐1 Machikaneyama‐choToyonakaOsaka560‐0043Japan
| | - Takanori Suzuki
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Central Research InstituteIshihara Sangyo Kaisha, Ltd.2‐3‐1 Nishi‐ShibukawaKusatsuShiga525‐0025Japan
| | - Hiro Takahashi
- Graduate School of Medical SciencesKanazawa UniversityKakuma‐machiKanazawaIshikawa920‐1192Japan
| | - Nanako Ishibashi
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
| | - Shoko Kojima
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Daisuke Kurihara
- JST, PRESTOFuro‐cho, Chikusa‐kuNagoyaAichi464‐8601Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
| | - Tetsuya Higashiyama
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
- Department of Biological SciencesGraduate School of ScienceUniversity of Tokyo7‐3‐1 Hongo, Bukyo‐kuTokyo113‐0033Japan
| | - Kotaro T. Yamamoto
- Division of Biological SciencesFaculty of ScienceHokkaido UniversitySapporo060‐0810Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Michiko Sasabe
- Department of BiologyFaculty of Agriculture and Life ScienceHirosaki University3 Bunkyo‐choHirosaki036‐8561Japan
| | - Yasunori Machida
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
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8
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Picart-Picolo A, Picault N, Pontvianne F. Ribosomal RNA genes shape chromatin domains associating with the nucleolus. Nucleus 2019; 10:67-72. [PMID: 30870088 PMCID: PMC6527388 DOI: 10.1080/19491034.2019.1591106] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genomic interactions can occur in addition to those within chromosome territories and can be organized around nuclear bodies. Several studies revealed how the nucleolus anchors higher order chromatin structures of specific chromosome regions displaying heterochromatic features. In this review, we comment on advances in this emerging field, with a particular focus on a recent study published by Quinodoz et al., that developed a new method to characterize simultaneous genomic interactions in the same cell. Highlighting studies conducted in animal and plant cells, we then discuss the establishment of inactive chromatin at nucleolus organizer region (NOR)-bearing chromosomes.
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Affiliation(s)
- Ariadna Picart-Picolo
- a CNRS , Laboratoire Génome et Développement des Plantes (LGDP) , Perpignan , France.,b Université de Perpignan Via Domitia , LGDP , Perpignan , France
| | - Nathalie Picault
- a CNRS , Laboratoire Génome et Développement des Plantes (LGDP) , Perpignan , France.,b Université de Perpignan Via Domitia , LGDP , Perpignan , France
| | - Frédéric Pontvianne
- a CNRS , Laboratoire Génome et Développement des Plantes (LGDP) , Perpignan , France.,b Université de Perpignan Via Domitia , LGDP , Perpignan , France
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9
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Abstract
The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes-inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist's perspective.
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Affiliation(s)
- Christian Schöfer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| | - Klara Weipoltshammer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
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10
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Carpentier MC, Picart-Picolo A, Pontvianne F. A Method to Identify Nucleolus-Associated Chromatin Domains (NADs). Methods Mol Biol 2018; 1675:99-109. [PMID: 29052188 DOI: 10.1007/978-1-4939-7318-7_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The nuclear context needs to be taken into consideration to better understand the mechanisms shaping the epigenome and its organization, and therefore its impact on gene expression. For example, in Arabidopsis, heterochromatin is preferentially localized at the nuclear and the nucleolar periphery. Although chromatin domains associating with the nuclear periphery remain to be identified in plant cells, Nucleolus Associated chromatin Domains (NADs) can be identified thanks to a protocol allowing the isolation of pure nucleoli. We describe here the protocol enabling the identification of NADs in Arabidopsis. Providing the transfer of a nucleolus marker as described here in other crop species, this protocol is broadly applicable.
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Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, CNRS, UMR5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Univ. Perpignan Via Domitia, UMR5096, 58 Ave P. Alduy, 66860, Perpignan, France
| | - Ariadna Picart-Picolo
- Laboratoire Génome et Développement des Plantes, CNRS, UMR5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Univ. Perpignan Via Domitia, UMR5096, 58 Ave P. Alduy, 66860, Perpignan, France
| | - Frédéric Pontvianne
- Laboratoire Génome et Développement des Plantes, CNRS, UMR5096, 66860, Perpignan, France.
- Laboratoire Génome et Développement des Plantes, Univ. Perpignan Via Domitia, UMR5096, 58 Ave P. Alduy, 66860, Perpignan, France.
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11
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Groves NR, Biel AM, Newman-Griffis AH, Meier I. Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals. PLANT PHYSIOLOGY 2018; 176:230-241. [PMID: 28739821 PMCID: PMC5761808 DOI: 10.1104/pp.17.00788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/17/2017] [Indexed: 05/19/2023]
Abstract
The functional organization of the plant nuclear pore, nuclear envelope, and nucleoplasm marks dynamically changing environmental cues and developmental programs.
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Affiliation(s)
- Norman R Groves
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Alecia M Biel
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Anna H Newman-Griffis
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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12
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Montacié C, Durut N, Opsomer A, Palm D, Comella P, Picart C, Carpentier MC, Pontvianne F, Carapito C, Schleiff E, Sáez-Vásquez J. Nucleolar Proteome Analysis and Proteasomal Activity Assays Reveal a Link between Nucleolus and 26S Proteasome in A. thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1815. [PMID: 29104584 PMCID: PMC5655116 DOI: 10.3389/fpls.2017.01815] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/06/2017] [Indexed: 05/23/2023]
Abstract
In all eukaryotic cells, the nucleolus is functionally and structurally linked to rRNA synthesis and ribosome biogenesis. This compartment contains as well factors involved in other cellular activities, but the functional interconnection between non-ribosomal activities and the nucleolus (structure and function) still remains an open question. Here, we report a novel mass spectrometry analysis of isolated nucleoli from Arabidopsis thaliana plants using the FANoS (Fluorescence Assisted Nucleolus Sorting) strategy. We identified many ribosome biogenesis factors (RBF) and proteins non-related with ribosome biogenesis, in agreement with the recognized multi-functionality of the nucleolus. Interestingly, we found that 26S proteasome subunits localize in the nucleolus and demonstrated that proteasome activity and nucleolus organization are intimately linked to each other. Proteasome subunits form discrete foci in the disorganized nucleolus of nuc1.2 plants. Nuc1.2 protein extracts display reduced proteasome activity in vitro compared to WT protein extracts. Remarkably, proteasome activity in nuc1.2 is similar to proteasome activity in WT plants treated with proteasome inhibitors (MG132 or ALLN). Finally, we show that MG132 treatment induces disruption of nucleolar structures in WT but not in nuc1.2 plants. Altogether, our data suggest a functional interconnection between nucleolus structure and proteasome activity.
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Affiliation(s)
- Charlotte Montacié
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Nathalie Durut
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Alison Opsomer
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Denise Palm
- Institute for Molecular Biosciences, Cluster of Excellence Macromolecular Complexes, Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Pascale Comella
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Frederic Pontvianne
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Cluster of Excellence Macromolecular Complexes, Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, UMR 5096, Perpignan, France
- Laboratoire Génome et Développement des Plantes, University of Perpignan Via Domitia, UMR 5096, Perpignan, France
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Merret R, Carpentier MC, Favory JJ, Picart C, Descombin J, Bousquet-Antonelli C, Tillard P, Lejay L, Deragon JM, Charng YY. Heat Shock Protein HSP101 Affects the Release of Ribosomal Protein mRNAs for Recovery after Heat Shock. PLANT PHYSIOLOGY 2017; 174:1216-1225. [PMID: 28381501 PMCID: PMC5462041 DOI: 10.1104/pp.17.00269] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
Heat shock (HS) is known to have a profound impact on gene expression at different levels, such as inhibition of protein synthesis, in which HS blocks translation initiation and induces the sequestration of mRNAs into stress granules (SGs) or P-bodies for storage and/or decay. SGs prevent the degradation of the stored mRNAs, which can be reengaged into translation in the recovery period. However, little is known on the mRNAs stored during the stress, how these mRNAs are released from SGs afterward, and what the functional importance is of this process. In this work, we report that Arabidopsis HEAT SHOCK PROTEIN101 (HSP101) knockout mutant (hsp101) presented a defect in translation recovery and SG dissociation after HS Using RNA sequencing and RNA immunoprecipitation approaches, we show that mRNAs encoding ribosomal proteins (RPs) were preferentially stored during HS and that these mRNAs were released and translated in an HSP101-dependent manner during recovery. By 15N incorporation and polysome profile analyses, we observed that these released mRNAs contributed to the production of new ribosomes to enhance translation. We propose that, after HS, HSP101 is required for the efficient release of RP mRNAs from SGs resulting in a rapid restoration of the translation machinery by producing new RPs.
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Affiliation(s)
- Rémy Merret
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.);
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Marie-Christine Carpentier
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Jean-Jacques Favory
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Claire Picart
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Julie Descombin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Cécile Bousquet-Antonelli
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Pascal Tillard
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Laurence Lejay
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Jean-Marc Deragon
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.);
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
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