BAF60/SWP73 Subunits Define Subclasses of SWI/SNF Chromatin Remodelling Complexes in Arabidopsis

• Evolutionarily conserved SWI-SNF ATP-dependent chromatin remodeling complexes (CRCs) change nucleosome positioning and chromatin states, affecting gene expression to regulate important regulatory processes controlling such as proper development and hormonal signalling pathways. • In our study we used transcript profiling, chromatin immunoprecipitation (ChIP), exhaustive protein-protein interaction study including mass-spectrometry, yeast-two-hybrid and bimolecular fluorescence complementation (BiFC) along with hormone and metabolite profiling, and phenotype assessments to distinguish the functions of Arabidopsis SWP73A and SWP73B subunits in Arabidopsis. • We identified a novel subclass of SWI/SNF chromatin remodelling complexes defined by the presence of SWP73A subunit. Therefore, we propose a refined classification of SWI/SNF CRCs in Arabidopsis, introducing BAS-A (SWP73A-containing) and BAS-B (SWP73B-containing) subclasses. The SWP73A and SWP73B-carrying subclasses of SWI/SNF CRCs exhibit differential properties demonstrated by distinct chromatin binding patterns and divergent effect on hormone biosynthesis and metabolism. We found that SWP73A plays a specific role that cannot be fully compensated by SWP73B. We recognized that some atypical subclasses of SWI/SNF CRCs may be likely formed in mutant lines with inactivated SWP73 subunits. • Our study reveals that the duplication of the SWP73 subunit contributes to unique and shared functions of subclasses of SWI/SNF CRCs in the control of various regulatory processes in Arabidopsis.