Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays

Sakamoto, Takuya; Sugiyama, Tomoya; Yamashita, Tomoe; Matsunaga, Sachihiro

doi:10.1080/19491034.2019.1616507

Cited by 19 publications

(25 citation statements)

References 43 publications

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“…Though positive spatial interactions with www.nature.com/scientificreports/ the nucleolus are unlikely to subtend our observations, the recently reported increased association of centromeric regions with the nucleolus in the nuc1 nucleolin mutant 63 raises the question of whether negative spatial interactions between CCs and the nucleolus may participate to the repulsive organization shown here. Other nuclear factors are likely involved, as suggested for example with recent studies reporting increased centromere association in mutants of plant condensin II subunits 64,65 .…”

Section: An Objective Demonstration Of Chromocenter Peripheral Locatimentioning

confidence: 90%

Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

Arpòn

Sakai

Gaudin

et al. 2021

Sci Rep

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The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions.

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Section: An Objective Demonstration Of Chromocenter Peripheral Locatimentioning

confidence: 90%

Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

Arpòn

Sakai

Gaudin

et al. 2021

Sci Rep

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“…CAP-D2 and CAP-D3 prevent the association of centromeres and induce chromatin compaction (Schubert et al, 2013). The requirement of the condensin II-specific subunits CAP-H2 and CAP-G2 for keeping centromeres apart has been confirmed by Sakamoto et al (2019). In addition, these authors showed that condensin II is necessary for the correct spatial arrangement between centromeres and rDNA arrays.…”

Section: Introductionmentioning

confidence: 91%

The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Municio

Antosz

Grasser

et al. 2019

Preprint

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Condensins are best known for their role in shaping chromosomes. However, other functions as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals. Yeasts encode one condensin complex, while higher eukaryotes have two of them (condensin I and II). Both, condensin I and II, are conserved in Arabidopsis thaliana, but so far little is known about their function. Here we show that the A. thaliana CAP-D2 (condensin I) and CAP-D3 (condensin II) subunits are highly expressed in mitotically active tissues. In silico and pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. Our data suggest that the expression, localization and composition of the condensin complexes in A. thaliana are similar as in other higher eukaryotes. Previous experiments showed that the lack of A. thaliana CAP-D3 leads to centromere association during interphase. To study the function of CAP-D3 in chromatin organization more in detail we compared the nuclear distribution of rDNA, of centromeric chromocenters and of different epigenetic marks, as well as the nuclear size between wild-type and cap-d3 mutants. In these mutants an association of heterochromatic sequences occurs, but nuclear size and the general methylation and acetylation patterns remain unchanged. In addition, transcriptome analyses revealed a moderate influence of CAP-D3 on general transcription, but a stronger one on transcription of stress-related genes. We propose a model for the CAP-D3 function during interphase, where CAP-D3 localizes in euchromatin loops to stiff them, and consequently separates centromeric regions and 45S rDNA repeats.

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“…3D). Furthermore condensin-2 has been recently implicated in controlling the association and dissociation of centromeres 65 . Additionally, we find an Fst outlier peak over CPg36347, homologue of DAYSLEEPER, an essential domesticated transposase 66 .…”

Section: Selective Sweeps Associated Specifically With Wgdmentioning

confidence: 99%

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

Bray

Wolf

Zhou

et al. 2020

Preprint

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Convergent evolution is observed broadly across the web of life, but the degree of evolutionary constraint during adaptation of core intracellular processes is not known. High constraint has been assumed for conserved processes, such as cell division and DNA repair, but reports of nimble evolutionary shifts in these processes have confounded this expectation. Whole genome duplication (WGD) necessitates the concerted adjustment of a wide range of fundamental intracellular functions but nevertheless has been repeatedly survived in all kingdoms. Given this repeated adaptation to WGD despite obvious intracellular challenges to core processes such as meiosis, we asked: how do lineages not only survive WGD, but sometimes ultimately thrive? Are the solutions employed constrained or diverse? Here we detect genes and processes under selection following WGD in the Cochlearia species complex by performing a scan for selective sweeps following WGD in a large-scale survey of 73 resequenced individuals from 23 populations across Europe. We then contrast our results from two independent WGDs in Arabidopsis arenosa and Cardamine amara. We find that while WGD does require the adaptation of particular functional processes in all three cases, the specific genes recruited to respond are highly flexible. We also observe evidence of varying degrees of convergence between different cases. Our results point to a polygenic basis for the distributed adaptive systems that control meiotic crossover number, ionomic rewiring, cell cycle control, and nuclear regulation. Given the sheer number of loci under selection post-WGD, we surmise that this polygenicity may explain the general lack of convergence between these species that are ~30 million years diverged. Based on our results, we speculate that adaptive processes themselves – such as the rate of generation of structural genomic variants—may be altered by WGD in nascent autopolyploids, contributing to the occasionally spectacular adaptability of autopolyploids observed across kingdoms.

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Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays

Cited by 19 publications

References 43 publications

Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

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