Rapid degradation of DHX36 revealing its transcriptional role by interacting with G‐quadruplex

Abstract Accumulating evidence indicates that G‐quadruplexes (G4s) are involved in transcriptional regulation. Previous studies have demonstrated that DHX36 preferentially resolves G4s, suggesting its potential impact on gene transcription mediated by these structures. However, systematic validation is required to establish a link between DHX36 activity and its roles in transcriptional regulation. In this study, we investigate the role of DHX36 in transcription. First, we employ the cleavage under targets and tagmentation (CUT&Tag), an efficient method for mapping protein–DNA interactions, to identify the binding sites in the chromatin of MCF‐7 cells. Subsequently, we use the auxin‐inducible degron (AID) protein degradation system and improved nascent RNA sequencing method acrylonitrile‐mediated uridine‐to‐cytidine conversion sequencing (AMUC‐seq) to pinpoint genes directly regulated by DHX36. Our results reveal a significant enrichment of G4 structures at DHX36 target sites, predominantly located in active genomic regions. In vitro assays further demonstrate DHX36's interaction with G4 sequences from three specific oncogenes. These findings underscore the potential role of DHX36 in modulating gene transcription through G4 structures.