Regulation of chromatin positioning in Arabidopsis thaliana

Abstract

The biochemical environment within the 3D nuclear space is not homogeneous. It has been demonstrated in many studies that the transcriptional activity of a gene is linked to its positioning inside the nuclear space. The NE not only serves as a physical barrier separating the nuclear content from the cytoplasm but also plays crucial roles in mediating the 3D organization of genomic DNA. Following the discovery of LADs, which are transcriptionally repressed chromatin regions, the non-random chromatin positioning at the NP and its biological relevance have been studied intensively in animals. However, it still remains unknown in plants that whether comparable chromatin organizations exist or not. In this study, RE-ChIP was used to reveal the genome-wide identification of non-random organization of chromatin domains positioned at the peripheral zone of Arabidopsis thaliana nuclei. The patterns of chromatin regions positioned at NP were similar across different tissues. These chromatin domains are enriched with silenced protein-coding genes, TE genes and heterochromatic marks, which collectively define a repressed environment at the NP. Furthermore, our results suggest a spatial compartment of different DNA methylation pathways that regulate TE silencing, where the CHH DNA methylation of TEs localized at the NP and in the nuclear interior is preferentially mediated by CMT2 and DRM methyltransferases, respectively. To elucidate how such chromatin positioning patterns at the NP was achieved in plants, dual-color FISH experiments were conducted to compare the difference of chromatin-NP interactions among various mutants. Our results show that in Arabidopsis thaliana, specific chromatin positioning at the NP requires plant lamin proteins CRWN1, CRWN4 and non-CG DNA methylation, which are all plant-specific. The result of chromosome painting indicates global attenuation of chromatin positioning patterns at the NP in both the crwn1 and crwn4 mutants. Moreover, ChIP-seq shows that CRWN1 directly interacts with chromatin regions localized at the NP. In summary, the NP is a functional sub-compartment enriched with heterochromatic domains. In addition, CRWN1 is a key component of lamin-chromatin network in plants. It is functionally equivalent to animals lamins, which play crucial roles in regulating chromatin positioning at the NP.