Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

Abstract

Background The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both plants and animals, the nuclear periphery is a functional compartment enriched with heterochromatin. To date, how plants manage to selectively tether chromatin at the nuclear periphery is unclear. Results By conducting dual-color fluorescence in situ hybridization experiments on 2C nuclei, we show that in Arabidopsis thaliana , specific chromatin positioning at the nuclear periphery requires plant lamin-like proteins CROWDED NUCLEI 1 (CRWN1), CRWN4, and DNA methylation in CHG and CHH contexts. With chromosome painting and Hi-C analyses, we show global attenuation of spatial chromatin compartmentalization and chromatin positioning patterns at the nuclear periphery in both the crwn1 and crwn4 mutants. Furthermore, ChIP-seq analysis indicates that CRWN1 directly interacts with chromatin domains localized at the nuclear periphery, which mainly contains non-accessible chromatin. Conclusions In summary, we conclude that CRWN1 is a key component of the lamina-chromatin network in plants. It is functionally equivalent to animal lamins, playing critical roles in modulating patterns of chromatin positioning at the nuclear periphery. Electronic supplementary material The online version of this article (10.1186/s13059-019-1694-3) contains supplementary material, which is available to authorized users.

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

“…This raises intriguing questions regarding the evolution of the structure and function of the nuclear periphery in plant and animal cells [1,14]. Nevertheless, peripheral chromatin regions called Plant Lamina-Associated Domains (PLADs) were identified first as chromatin regions associated with NUP1/136, a component of the nuclear pore complex [15] and more recently with CRWN1, a component of the nucleoskeleton [16]. Like in animal cells, the nucleoskeleton of the plant nucleus may function to tether chromatin domainsas seen by ChIP and chromosome painting-that carry repressive features [15,16].…”

“…Nevertheless, peripheral chromatin regions called Plant Lamina-Associated Domains (PLADs) were identified first as chromatin regions associated with NUP1/136, a component of the nuclear pore complex [15] and more recently with CRWN1, a component of the nucleoskeleton [16]. Like in animal cells, the nucleoskeleton of the plant nucleus may function to tether chromatin domainsas seen by ChIP and chromosome painting-that carry repressive features [15,16]. Peripheral localisation of these domains seems dependent upon non-CG methylation [16], a DNA modification unique to plants, hence representing plant-specific novelties in LAD regulation and function.…”

“…Like in animal cells, the nucleoskeleton of the plant nucleus may function to tether chromatin domainsas seen by ChIP and chromosome painting-that carry repressive features [15,16]. Peripheral localisation of these domains seems dependent upon non-CG methylation [16], a DNA modification unique to plants, hence representing plant-specific novelties in LAD regulation and function.…”

“…In addition, there is an increasing interest in analysing the positioning of loci relative to chromosome territories or to the nuclear periphery to establish the functional link between gene activity and locus positioning. Yet, analyses have so far considered only 2D nuclei models [16,23,122]. To address the question in the real 3D space of the nucleus it is necessary to retrieve spatial distance information.…”

“…To address the question in the real 3D space of the nucleus it is necessary to retrieve spatial distance information. Some image analysis solutions are beginning to be proposed for this [123], and recent 2D spatial positioning scoring systems [16] should be developed in 3D in the near future. Recording the relative position of transcription loci, topological domains, peripheral domain proteins etc.…”