Impact of histone N-terminal domains and linker DNA on H2A.Z deposition by yeast SWR1C

ATP-dependent chromatin remodeling enzymes play a central role in governing the essential functions of the genome, and deficiencies in their catalytic function often lead to developmental disorders or disease. While most remodelers use the energy of ATP hydrolysis to either mobilize nucleosomes or evict histone octamers, yeast SWR1C catalyzes the ATP-dependent replacement of nucleosomal H2A/H2B dimers with variant H2A.Z/H2B dimers. The H2A.Z histone variant is conserved in all eukaryotes where it plays key roles in regulating gene transcription, DNA repair, and heterochromatin function. Consequently, the regulation of H2A.Z deposition by SWR1C is central to numerous genomic functions. Here, we use both quantitative fluorescence-based assays and gel-based, electrophoretic methods to dissect the roles of histone tails, histone acetylation, and linker DNA in SWR1C-mediated H2A.Z deposition in vitro. Unlike many other remodeling enzymes, we find that histone tails are largely dispensable for the catalytic activity of SWR1C, and histone acetylation by the NuA4 acetyltransferase has only a minor stimulatory impact on SWR1C activity. In contrast, we confirm previous studies that nucleosome-free, linker DNA stimulates SWR1C activity even under saturating enzyme levels. These insights provide a clearer understanding of the structural and regulatory determinants that guide H2A.Z deposition by SWR1C, offering potential new avenues to investigate its role in chromatin dynamics and genome stability.