The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Abstract

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.

Helical metaphase chromatid coiling is conserved

“…Paulson and Laemmli (1977) suggested a ‘scaffold model’ based on histone-depleted human chromosomes with a non-histone protein backbone responsible for chromatin looping and chromosome condensation. Topoisomerase IIα and the Structural Maintenance of Chromosomes (SMC) complexes condensin I and II are components of the scaffold in Drosophila (Sureka et al, 2018), chicken (Ohta et al, 2019) and human (Maeshima and Laemmli, 2003; Fukui and Uchiyama 2007; Maeshima et al, 2018; Walther et al, 2018), and are also evident in Arabidopsis and barley (Kubalová et al, 2021; Municio et al, 2021). In human HeLa cells the chromatid axes appear as isolated compaction centers rather than forming a continuous scaffold (Sun et al 2018), and appear to consist of a helical structure that serves to organize chromatin loops into the metaphase chromatid (Phengchat et al, 2019).…”

The Role of Structural Maintenance of Chromosomes Complexes in Meiosis and Genome Maintenance: Translating Biomedical and Model Plant Research Into Crop Breeding Opportunities

“…Eukaryotes have three sets of canonical SMC protein complexes ( Municio et al, 2021 ): (1) the cohesin complex composed of the core proteins SMC1 and SMC3, mentioned previously, mostly involved in sister chromatid cohesion; (2) the SMC5/SCM6 complex, which is mostly linked to DNA repair and recombination; and (3) the condensin complex, which is composed of core units SMC2 and SMC4 and is required for chromosome condensation and segregation ( Sakamoto et al, 2019 ).…”

“…The plant condensin complex I consists of core units SMC2/SMC4, γ-kleisin (CAP)-H, β-kleisin (CAP)-H2, and HEAT repeat-containing proteins CAP-G and CAP-D2. However, the association of SMC2/SMC4 with CAP-H2 (β-kleisin), CAP-G2, and CAP-D3 form condensin II ( Sakamoto et al, 2019 ; Municio et al, 2021 ), a complex that may be required for tolerance to DSBs caused by the radiomimetic agent zeocin for tolerance to boron ( Sakamoto et al, 2011 ; see Figure 5 ). In Arabidopsis , defects in the function of SMC2 (2 genes) or SMC4 (3 genes) affect segregation of mitotic and meiotic chromosomes ( Sakamoto et al, 2019 ).…”

“…The Arabidopsis condensin II complex is also required for genome integrity and for pollen and embryo development ( Schubert et al, 2013 ; Sakamoto et al, 2019 ; Municio et al, 2021 ). A combined spatial analysis of the localization of the 180-bp centromeric repeat and the 5S and 45S rDNA probes was performed in the Arabidopsis cap-h2-2 , cap-g2-1 , and cap-d3-1 mutants (see Figure 5 ).…”

“…Results indicated disassociation of the rDNA arrays from the centromeres, thus suggesting that direct binding of condensin II to rDNA array regions is necessary for their association with centromeres in A. thaliana ( Sakamoto et al, 2019 ). However, cytological analysis of Arabidopsis cap-d3 interphase nuclei indicated specific clustering of 45 rDNA sites, so CAP-D3 might localize in euchromatic loops and somehow determine the rigidity needed to maintain separation of chromocenters ( Municio et al, 2021 ) In any case, an analysis of 3D chromatin organization by Hi-C may help clarify the distribution pattern of condensin II during interphase and its role in the clustering of rDNA arrays during interphase ( Sakamoto et al, 2019 ). Evidence also indicates that SMC4/condensin is required for repression of a wide range of methylated genes subject to conditional expression ( Wang et al, 2017 ).…”