Replication‐coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development

Abstract

Developmental phase transitions are often characterized by changes in the chromatin landscape and heterochromatin reorganization. In Arabidopsis, clustering of repetitive heterochromatic loci into so-called chromocenters is an important determinant of chromosome organization in nuclear space. Here, we investigated the molecular mechanisms involved in chromocenter formation during the switch from a heterotrophic to a photosynthetically competent state during early seedling development. We characterized the spatial organization and chromatin features at centromeric and pericentromeric repeats and identified mutant contexts with impaired chromocenter formation. We find that clustering of repetitive DNA loci into chromocenters takes place in a precise temporal window and results in reinforced transcriptional repression. Although repetitive sequences are enriched in H3K9me2 and linker histone H1 before repeat clustering, chromocenter formation involves increasing enrichment in H3.1 as well as H2A.W histone variants, hallmarks of heterochromatin. These processes are severely affected in mutants impaired in replication-coupled histone assembly mediated by CHROMATIN ASSEMBLY FACTOR 1 (CAF-1). We further reveal that histone deposition by CAF-1 is required for efficient H3K9me2 enrichment at repetitive sequences during chromocenter formation. Taken together, we show that chromocenter assembly during post-germination development requires dynamic changes in nucleosome composition and histone post-translational modifications orchestrated by the replication-coupled H3.1 deposition machinery.

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

“…Image segmentation of nuclear signals detected as distinct objects is used to characterise them in terms of their geometrical features (size, shape, smoothness) and their number and positions, either relative to each other or in the image coordinate system. For instance, measuring the size, shape and distribution of chromocenters in Arabidopsis nuclei has been a useful indicator to elucidate the role of nuclear envelope proteins or histone chaperones in nuclear morphology and chromatin organisation [118][119][120] (Figure 4(b1)). Furthermore, once signals-of-interest are segmented, their relative distribution, e.g.…”

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

“…Histone modifications also appear involved in fine‐tuning different phases of plant development. They can, for example, influence flowering time (Crevillen et al , 2019) and the switch from the heterotrophic to the photosynthetic stages during early seedling development in Arabidopsis (Benoit et al , 2019). Through the use of mutants and crossing experiments a further study by Zhao et al .…”

Disruption ofNAP1genes supresses thefas1mutant phenotype and enhances genome stability

“…CAF-1 is an H3.1 histone chaperone and its deficiency can, at least partially, be compensated for by HIRA or ATRX complementary pathways, as shown recently (Duc et al, 2015; Duc et al, 2017). This compensation, however, affects the ratio of H3.1/H3.3, otherwise important for correct chromatin assembly and the epigenetic set up during early development (Otero et al, 2016; Benoit et al, 2019). The altered H3.1 loading and H3.1/H3.3 imbalance, as observed in fas1, relates to the: i) lower abundance of nucleosomes, particularly in non-transcribed regions (Munoz-Viana et al, 2017); ii) decreased levels of H3K27me1 histone mark (Jacob et al, 2014; Wollmann et al, 2017); iii) instability of 45S rDNA and telomere repeats and decondensation of chromocenters (Kirik et al, 2006; Mozgova et al, 2010; Varas et al, 2015); and/or iv) changes in the transcription level of a selected set of genes (Bouveret et al, 2006; Ramirez-Parra and Gutierrez, 2007; Mozgova et al, 2015).…”

“…Moreover, NAP1 is considered to be an H2A/H2B histone chaperone in plants and such an alteration could be expected at the level of H2 turnover or even other protein complexes. An interesting candidate could be the H2A.W variant, important for heterochromatin formation and internal DNA damage repair (Yelagandula et al, 2014), whose levels were shown to drop in fas1 (Benoit et al, 2019). Moreover, we show that individual NAP1 genes are upregulated in fas1, potentially causing an imbalance during chromatin assembly in fas1 .…”