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

Georgia Chatzinikolaou1, Kalliopi Stratigi1, Athanasios Siametis1,2

  • 1Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece.

Science Advances
|November 8, 2023
PubMed
Summary
This summary is machine-generated.

This study reveals how RNA-DNA hybrids (R-loops) are processed during transcription. The nucleotide excision repair factor XPF, with TOP2B and CTCF/cohesin, facilitates R-loop resolution, impacting DNA looping and gene activation.

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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.