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

ABSTRACT: DNA replication encounters obstacles such as stalled transcription complexes and R-loops. 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. Genome-wide DRIP analyses further reveal significant R-loop accumulation at highly expressed genes. Together, these findings identify SMARCAD1 as an early responder to R-loop-mediated transcription-replication conflicts (TRCs) that safeguards the integrity of active replication forks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE339312 | GEO | 2026/09/22

REPOSITORIES: GEO

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