Structural basis for the non-canonical nucleosome remodeling by ATRX

Alpha-thalassemia/mental retardation syndrome X-linked (ATRX) is a sucrose nonfermentable 2 (Snf2)-family ATP-dependent chromatin remodeler essential for chromatin regulation and genome stability, but its remodeling mechanism remains unclear. Here, we report three structures of the human ATRX ATPase domain (ATRX_ATPase) in its free, nucleosome-bound, and histone-bound states, revealing a non-canonical mechanism of activity regulation and chromatin remodeling. ATRX_ATPase adopts a structurally primed but autoinhibited conformation that is relieved upon nucleosome binding. ATRX favors ATP-dependent nucleosome disassembly over sliding and engages a non-canonical nucleosomal site, contacting unwrapped DNA at superhelical location (SHL) 5.5-7. An ATRX-specific histone-binding motif contributes to ATPase-driven nucleosome disassembly and also binds H3-H4, cooperating with ASF1 to promote tetrasome assembly. Genome-wide analyses further indicate that ATRX associates with active chromatin independently of death domain-associated protein (DAXX) and contributes to chromatin accessibility at intergenic regulatory elements. These findings define ATRX as a mechanistically distinct remodeler that couples disassembly-biased remodeling to histone chaperoning, thereby supporting dynamic chromatin regulation.