Functional role of domains in the Snf2 subunit of the SWI/SNF complex outside the catalytic domain

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SWI/SNF is the classical ATP dependent chromatin remodeler that restructures nucleosomes by virtue of its DNA and nucleosome stimulated ATPase activity. In this context, much attention has been devoted to the biochemical and genetic analyses of the ATPase‐helicase domain of the catalytic subunit Snf2. The catalytic contribution of the regions outside this domain has been explored to a limited extent, mostly focusing on the C terminal bromodomain. In this study, we use bioinformatic tools to identify putative domains in Snf2 (N, QLQ, spacer and AT), selectively delete them and characterize the domain deleted complexes both in vitro and in vivo. Our results indicate that complex integrity is preserved in the absence of these domains. Deletion of N terminus and the double AT hook show no difference in activity in vitro although these deletions have a snf2 null global gene expression pattern. In contrast, "QLQ" and "spacer" deletions are catalytically defective both in vitro and in vivo. In vitro, they show poor ATP hydrolysis and remodeling capacity. In vivo, they closely mimic snf2 null phenotype. Site directed DNA and histone crosslinking studies identify subtle conformational changes in presence of these deletions that may perturb proper nucleosomal contacts critical for remodeling. In summary, regions outside the ATPase‐helicase domain of Snf2 contribute positively to the catalytic function of the holocomplex.