Mechanistic insights into chromatin modulation by the orphan remodeler ATRX

Alpha-thalassemia/mental retardation syndrome X-linked protein (ATRX) is an ATP-dependent chromatin remodeler that performs diverse functions, including spacing nucleosomes, facilitating the deposition of histone variant H3.3, and preventing replication stress. The mechanism by which ATRX modulates chromatin is unknown. Here, our cryo-EM structure revealed that ATRX recognizes and modulates the nucleosome through its C-terminal regions by embracing and unwrapping [~]18 base-pair nucleosomal DNA near the entry/exit sites in the presence of ADP*BeF3. Strikingly, the DNA minor groove between SHL6 and SHL7 is profoundly deformed by a "pin-like" structure in ATRX, which uniquely intercalates the aromatic side chain of a phenylalanine into the base stackings. Biochemical assays revealed the crucial role of this phenylalanine in sliding the nucleosome without affecting the ATPase activity. Such a "pin-like" structure mimics a "foot-step" on the DNA ladder, which differentiates ATRX from other remodelers. To translocate the DNA on the nucleosome, two more features, including a disordered insertion that contacts the histone surface and a positively charged loop bridging the cross-gyre interactions, serve as essential anchors for the nucleosome modulation by ATRX. Together, we propose a "climbing" model for how ATRX mobilizes the DNA upon ATP hydrolysis.