Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome.

Abstract

The histone variant H2A.Z marking permissive chromatin is deposited by the multicomponent SWR1 chromatin remodeler, which is targeted to nucleosome-free promoters by a DNA length-sensing module. How SWR1 is directed to the flanking acetylated +1 nucleosome, its physiological substrate, has been enigmatic. We show by live-cell, single-molecule tracking that SWR1 subunits Bdf1 and Yaf9 harboring histone acetylation reader domains differentially regulate chromatin binding: Bdf1 promotes SWR1 association, while Yaf9-YEATS slows its dissociation. Notably, single-molecule tracking and genome-wide chromatin immunoprecipitation combined with exonuclease treatment reveal Bdf1 and Yaf9 contributions to global SWR1 targeting and histone exchange at +1 nucleosomes. Our findings highlight the in-cell biochemistry of histone readers and suggest a generalizable, two-stage mechanism wherein acetylated nucleosome interactions initially constrain the three-dimensional diffusion of SWR1 to increase local concentration, followed by stochastic one-dimensional diffusion at nucleosome-depleted regions with directional capture by acetylated +1 nucleosomes.