SMARCAD1 Acts as an Early R-loop Responder at Active Replication Forks

Although ribonucleases and DNA–RNA helicases remove these obstacles from genomic DNA, it remains understudied how this occurs in a chromatin context. Using in vitro and cellular approaches, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, resolves R-loops near nascent DNA to maintain fork stability.

SMARCAD1 binds DNA–RNA hybrids and R-loop structures in vitro, and its ATPase-dependent catalytic activity promotes R-loop resolution when tethered to an R-loop hotspot locus. SMARCAD1 binds R-loops through its ATPase domain and associates with the replisome through its N-terminal region, with both interactions required for efficient R-loop resolution in-cells. Quantitative image-based cytometry, single-molecule chromatin-fiber and proximity-labeling assays show that R-loops significantly accumulate near nascent DNA in SMARCAD1 mutant cells.