Chromatin remodeling complexes regulate genome architecture in Arabidopsis

We examined the 3D chromatin structure within the ATPase subunit of SWI/SNF, ISWI, INO80 and CHD remodeling complexes in wild-type (WT) and mutant plants by combining high throughput sequencing with in situ Hi-C, the enrichment of histone marks, nucleosome density and gene expression. Compartmental strength was significantly weakened in all four enzyme mutants, and particularly in compartment switching. Chromatin remodeling complexes differentially regulated nucleosome distribution pattern and density within the switching compartments. Alteration of nucleosome distribution pattern and density caused a reduction in H3K27me3 levels in the chromatin remodeling enzyme mutants, and led to compartment switching.