1
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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2
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Nowicka A, Ferková Ľ, Said M, Kovacik M, Zwyrtková J, Baroux C, Pecinka A. Non-Rabl chromosome organization in endoreduplicated nuclei of barley embryo and endosperm tissues. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2527-2541. [PMID: 36705553 DOI: 10.1093/jxb/erad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 06/06/2023]
Abstract
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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Affiliation(s)
- Anna Nowicka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ľuboslava Ferková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
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3
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Gent JI, Higgins KM, Swentowsky KW, Fu FF, Zeng Y, Kim DW, Dawe RK, Springer NM, Anderson SN. The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm. THE PLANT CELL 2022; 34:3685-3701. [PMID: 35775949 PMCID: PMC9516051 DOI: 10.1093/plcell/koac199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Demethylation of transposons can activate the expression of nearby genes and cause imprinted gene expression in the endosperm; this demethylation is hypothesized to lead to expression of transposon small interfering RNAs (siRNAs) that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maize (Zea mays) maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis thaliana DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting is its main function in endosperm.
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Affiliation(s)
| | - Kaitlin M Higgins
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Dong won Kim
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
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4
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Yadav VK, Santos-González J, Köhler C. INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis. Nucleic Acids Res 2021; 49:4371-4385. [PMID: 33744975 PMCID: PMC8096224 DOI: 10.1093/nar/gkab191] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/10/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022] Open
Abstract
Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.
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Affiliation(s)
- Vikash Kumar Yadav
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
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5
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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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6
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Golczyk H, Limanówka A, Uchman-Książek A. Pericentromere clustering in Tradescantia section Rhoeo involves self-associations of AT- and GC-rich heterochromatin fractions, is developmentally regulated, and increases during differentiation. Chromosoma 2020; 129:227-242. [PMID: 32681184 PMCID: PMC7666280 DOI: 10.1007/s00412-020-00740-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
A spectacular but poorly recognized nuclear repatterning is the association of heterochromatic domains during interphase. Using base-specific fluorescence and extended-depth-of-focus imaging, we show that the association of heterochromatic pericentromeres composed of AT- and GC-rich chromatin occurs on a large scale in cycling meiotic and somatic cells and during development in ring- and bivalent-forming Tradescantia spathacea (section Rhoeo) varieties. The mean number of pericentromere AT-rich domains per root meristem nucleus was ca. half the expected diploid number in both varieties, suggesting chromosome pairing via (peri)centromeric regions. Indeed, regular pairing of AT-rich domains was observed. The AT- and GC-rich associations in differentiated cells contributed to a significant reduction of the mean number of the corresponding foci per nucleus in relation to root meristem. Within the first 10 mm of the root, the pericentromere attraction was in progress, as if it was an active process and involved both AT- and GC-rich associations. Complying with Rabl arrangement, the pericentromeres preferentially located on one nuclear pole, clustered into diverse configurations. Among them, a strikingly regular one with 5-7 ring-arranged pericentromeric AT-rich domains may be potentially engaged in chromosome positioning during mitosis. The fluorescent pattern of pachytene meiocytes and somatic nuclei suggests the existence of a highly prescribed ring/chain type of chromocenter architecture with side-by-side arranged pericentromeric regions. The dynamics of pericentromere associations together with their non-random location within nuclei was compared with nuclear architecture in other organisms, including the widely explored Arabidopsis model.
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Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of Biological Sciences, John Paul II Catholic University of Lublin, Konstantynów 1i, 20-708, Lublin, Poland.
| | - Arleta Limanówka
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
| | - Anna Uchman-Książek
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
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7
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3-D Nucleus Architecture in Oat × Maize Addition Lines. Int J Mol Sci 2020; 21:ijms21124280. [PMID: 32560105 PMCID: PMC7352526 DOI: 10.3390/ijms21124280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids.
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8
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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] [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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9
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Koláčková V, Perničková K, Vrána J, Duchoslav M, Jenkins G, Phillips D, Turkosi E, Šamajová O, Sedlářová M, Šamaj J, Doležel J, Kopecký D. Nuclear Disposition of Alien Chromosome Introgressions into Wheat and Rye Using 3D-FISH. Int J Mol Sci 2019; 20:ijms20174143. [PMID: 31450653 PMCID: PMC6747102 DOI: 10.3390/ijms20174143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 01/07/2023] Open
Abstract
During interphase, the chromosomes of eukaryotes decondense and they occupy distinct regions of the nucleus, called chromosome domains or chromosome territories (CTs). In plants, the Rabl’s configuration, with telomeres at one pole of nucleus and centromeres at the other, appears to be common, at least in plants with large genomes. It is unclear whether individual chromosomes of plants adopt defined, genetically determined addresses within the nucleus, as is the case in mammals. In this study, the nuclear disposition of alien rye and barley chromosomes and chromosome arm introgressions into wheat while using 3D-FISH in various somatic tissues was analyzed. All of the introgressed chromosomes showed Rabl’s orientation, but their relative positions in the nuclei were less clear. While in most cases pairs of introgressed chromosomes occupied discrete positions, their association (proximity) along their entire lengths was rare, and partial association only marginally more frequent. This arrangement is relatively stable in various tissues and during various stages of the cell cycle. On the other hand, the length of a chromosome arm appears to play a role in its positioning in a nucleus: shorter chromosomes or chromosome arms tend to be located closer to the centre of the nucleus, while longer arms are more often positioned at the nuclear periphery.
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Affiliation(s)
- Veronika Koláčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Kateřina Perničková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales SY23 3DA, UK
| | - Dylan Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales SY23 3DA, UK
| | - Edina Turkosi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462 Martonvásár, P.O. Box 19, Hungary
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic.
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10
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Roth M, Florez-Rueda AM, Paris M, Städler T. Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1084-1101. [PMID: 29953688 DOI: 10.1111/tpj.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/01/2018] [Accepted: 06/20/2018] [Indexed: 05/06/2023]
Abstract
Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome-wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular-type endosperm development are lacking. Using laser-assisted microdissection, we characterized parent-specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear-type endosperm. Forty-two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression-level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular- and nuclear-type endosperm.
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Affiliation(s)
- Morgane Roth
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
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11
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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12
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Arpòn J, Gaudin V, Andrey P. A Method for Testing Random Spatial Models on Nuclear Object Distributions. Methods Mol Biol 2018; 1675:493-507. [PMID: 29052210 DOI: 10.1007/978-1-4939-7318-7_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The cell nucleus is a structurally complex and dynamic organelle ensuring key biological functions. Complex relationships between nuclear structure and functions require a better understanding of the three-dimensional organization of the genome and of the subnuclear compartments. Quantitative image analysis coupled with spatial statistics and modeling is a relevant approach to address these questions. In this chapter, we describe a step-by-step procedure to process images and to test a spatial random model for the distribution of nuclear objects using chromocenters as an example. More elaborate models can be designed on the basis of the random model by introducing additional and more complex constraints to better fit observations and to question determinants of these spatial organizations.
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Affiliation(s)
- Javier Arpòn
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France.
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13
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Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
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Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
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14
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Abstract
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis. Although many of these aspects are less well understood for the nuclei of plants than for those of animals or fungi, several recent discoveries have begun to place our understanding of plant nuclei firmly into this broader cell-biological context.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
| | | | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
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15
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Skinner BM, Johnson EEP. Nuclear morphologies: their diversity and functional relevance. Chromosoma 2017; 126:195-212. [PMID: 27631793 PMCID: PMC5371643 DOI: 10.1007/s00412-016-0614-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/17/2016] [Indexed: 12/20/2022]
Abstract
Studies of chromosome and genome biology often focus on condensed chromatin in the form of chromosomes and neglect the non-dividing cells. Even when interphase nuclei are considered, they are often then treated as interchangeable round objects. However, different cell types can have very different nuclear shapes, and these shapes have impacts on cellular function; indeed, many pathologies are linked with alterations to nuclear shape. In this review, we describe some of the nuclear morphologies beyond the spherical and ovoid. Many of the leukocytes of the immune system have lobed nuclei, which aid their flexibility and migration; smooth muscle cells have a spindle shaped nucleus, which must deform during muscle contractions; spermatozoa have highly condensed nuclei which adopt varied shapes, potentially associated with swimming efficiency. Nuclei are not passive passengers within the cell. There are clear effects of nuclear shape on the transcriptional activity of the cell. Recent work has shown that regulation of gene expression can be influenced by nuclear morphology, and that cells can drastically remodel their chromatin during differentiation. The link between the nucleoskeleton and the cytoskeleton at the nuclear envelope provides a mechanism for transmission of mechanical forces into the nucleus, directly affecting chromatin compaction and organisation.
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Affiliation(s)
- Benjamin M Skinner
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
| | - Emma E P Johnson
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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