XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Co-transcriptional RNA-DNA hybrids (R-loops) pose risks to genome integrity by causing DNA damage.
• The precise mechanisms by which R-loops regulate gene activity remain largely unknown.

Purpose of the Study:

• To elucidate the molecular mechanisms underlying R-loop processing during transcription.
• To investigate the role of the nucleotide excision repair factor XPF in R-loop resolution and gene regulation.

Main Methods:

• Co-immunoprecipitation assays to identify protein interactions.
• Chromatin immunoprecipitation (ChIP) to assess protein recruitment to gene promoters.
• Analysis of DNA damage response markers and DNA looping.

Main Results:

• XPF interacts with CTCF and cohesin subunits (SMC1A, SMC3), mediating R-loop-dependent DNA looping during transcription activation.
• XPF recruits TOP2B to active gene promoters, promoting double-strand breaks and DNA damage response activation.
• TOP2B abrogation impairs the recruitment of XPF, CTCF, and cohesin, hindering DNA looping and R-loop processing.

Conclusions:

• XPF, TOP2B, and the CTCF/cohesin complex are crucial for processing R-loops during transcription activation.
• This pathway is vital for maintaining genome integrity and regulating gene expression.
• Findings have implications for understanding DNA repair-deficient syndromes linked to transcription-associated DNA damage.