The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

Poulet, Axel; Duc, Céline; Voisin, Maxime; Desset, Sophie; Tutois, Sylvie; Vanrobays, Emmanuel; Benoit, Matthias; Evans, David; Probst, Aline V.; Tatout, Christophe

doi:10.1242/jcs.194712

Cited by 71 publications

(82 citation statements)

References 81 publications

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“…(See Box 1 for expansion of abbreviated gene names used in this review.) In addition, the association of heterochromatin domains with the LINC (linker of nucleoskeleton and cytoskeleton) complex in the nuclear periphery is a spatial component that is relevant for heterochromatin silencing, as revealed using loss-of-function mutants [34]. The RdDM pathway, which relies on RNA Pol IV-dependent 24-nucleotide short interfering RNAs (siRNAs) [35–37] and RNA Pol V-dependent RNAs [38], is crucial for both preserving the boundaries of heterochromatin domains and keeping TEs silent across generations [18, 39–41].…”

Section: Genome Topographymentioning

confidence: 99%

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Vergara

Gutiérrez

2017

Genome Biol

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Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility. Current studies reinforce the idea of intimate crosstalk between chromatin features and processes involving DNA transactions.

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Section: Genome Topographymentioning

confidence: 99%

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Vergara

Gutiérrez

2017

Genome Biol

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“…Christophe Tatout (Université Clermont Auvergne, France) gave the final talk in the workgroup 1 session and outlined his work that focuses on developing NucleusJ, an ImageJ plugin for 3D analysis of nucleus images; it is now being improved and adapted to perform high-throughput 3D image analysis (Poulet et al, 2017) of different nuclear parameters, such as size and shape of the nucleus, and the position of heterochromatin structures within in the nucleus in whole-mount tissues. Efficient phenotyping tools are indispensable assets to evaluate the impact of loss of specific nuclear components, such as components of the nuclear periphery, on, for example, nuclear organisation and function.…”

Section: The Origins and Aims Of Indepthmentioning

confidence: 99%

Meeting report – INDEPTH kick-off meeting

et al. 2018

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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.The kick-off meeting of the INDEPTH consortium revolved around an exciting overall theme of an increased appreciation about how gene expression can be affected by the sequestering of loci within different nuclear compartments. The meeting showed promising technological advances that will overcome challenges particular to plant tissues both in the detection of single-locus positions and in dedicated image analysis. Another emerging theme is the development of new approaches that will combine information gained from microscopic images that provide single-cell resolution with the information that is gained from conformation-capture techniques that represent an average view of multiple cells in a tissue. Together with the characterisation of nuclear structures that are specific to plants, these techniques will allow this community to gain insight into the plant-specific mechanisms of gene expression control and to compare and contrast these with the mechanisms identified in yeast and mammalian model organisms. Organisation of the INDEPTH consortiumA key component of the INDEPTH COST Action (Box 1) is its organisation into five complementary workgroups (Fig. 1), whose activities were introduced at the kick-off meeting. Three of the workgroups focus on evaluating plant chromatin domains at different scales, from imaging nuclear domains (workgroup 1) through analysis of the function of chromatin domains in controlling gene expression (workgroup 2) to assessing their effect on plant phenotypes and their dynamics during stresses (workgroup 3). Workgroup 4 is involved in tackling the challenge of storage and sharing of 'omics'-based and image data, something that has relevance to a much wider community of researchers beyond the INDEPTH consortium, and workgroup 5 organises training and dissemination of INDEPTH outputs from each of the other four workgr...

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“…Toward that goal, Poulet et al (2017a) have developed a 3D imaging protocol to query a number of aspects of nuclear and chromatin organization in Arabidopsis mutants of LINC complex components and related proteins. They found that chromocenters were preferentially associated with the nuclear periphery, but that this association and chromocenter compaction were changed in some mutants.…”

Section: The Nuclear Peripherymentioning

confidence: 99%

“…They found that chromocenters were preferentially associated with the nuclear periphery, but that this association and chromocenter compaction were changed in some mutants. Interestingly, transcriptional repression of heterochromatic repeat sequences was alleviated in some LINC mutants, suggesting that the Arabidopsis nuclear periphery is indeed involved in regulatory chromatin compaction (Poulet et al, 2017a).…”

Section: The Nuclear Peripherymentioning

confidence: 99%

Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals

et al. 2017

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ORCID ID: 0000-0002-4141-5400 (I.M.).In both plants and animals, the nucleus acts as an organizing center for the changes that occur during an organism's life cycle, whether as part of a developmental program or in response to environmental factors. Here, we cover recent research that explores roles of the nucleus other than gene expression in light response, fertilization, plant-pathogen interactions, bacterial symbiotic events, and hormone signaling. New strides have been made in understanding subnuclear organization, how nuclear organization responds to different environments and developmental stages, and how the cytoplasm-nucleoplasm connections are made that allow these responses. We further highlight new tools that have been developed to study dynamic changes in nuclear organization.The nucleus is compartmentalized by a double membrane called the nuclear envelope (NE), which consists of the outer nuclear membrane (ONM), the inner nuclear membrane (INM), and the embedded nuclear pore complexes (NPCs). The NPC is the primary pathway of macromolecular transport between the nucleus and the cytoplasm and is conserved throughout eukaryotes. The ONM and INM are populated by a variety of membrane-associated proteins, and in particular the inner membrane hosts a specific subset of proteins (Starr and Fridolfsson, 2010;Meier et al., 2017). In addition to functioning in nuclear morphology, chromatin attachment, and likely signal transduction, plant NE-associated proteins are involved in nuclear positioning and movement within the larger cellular context (Griffis et al., 2014). While plant nuclear ultrastructure reveals an inner nuclear membrane-associated meshwork similar to the animal lamina, plant genomes do not encode obvious lamin homologs. Instead, plant-specific long coiled-coil proteins with structural similarity to animal lamins might contribute to this meshwork. Plants also lack centrosomes, and the NE plays a role as the microtubuleorganizing center at the onset of mitosis. NE proteins functioning as calcium channels are involved in perinuclear calcium oscillations, which are an important step in the establishment of plant-symbiont interactions (recently reviewed in Meier et al., 2017).While the nuclear periphery is emerging as an essential organizing platform for the nucleus, intranuclear functional and structural organization might also originate from independent self-assembly processes, with the most conspicuous manifestation of these processes revealed as the nucleolus. New methods are now robustly adapted for plants to reveal greater details of functional nuclear and nucleolar organization. Due to the increasing realization that spatial organization is a crucial part of biological function at the subcellular level, many of these aspects have been recently reviewed

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The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

Cited by 71 publications

References 81 publications

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Meeting report – INDEPTH kick-off meeting

Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals

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