APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer

Area of Science:

• Molecular Biology
• Genetics
• Cancer Research

Background:

• APOBEC3B is a single-stranded DNA deaminase with roles in antiviral defense and cancer.
• Its cellular substrates and functions, particularly in cancer, remain incompletely understood.

Purpose of the Study:

• To investigate the cellular substrates and functions of APOBEC3B, focusing on its potential role in R-loop regulation and cancer mutagenesis.
• To elucidate the mechanism by which APOBEC3B influences R-loop dynamics and contributes to genomic instability.

Main Methods:

• Proteomics to identify APOBEC3B interacting partners.
• Biochemical assays to confirm APOBEC3B binding to R-loops in vitro and in cells.
• Genetic manipulation (knockout and overexpression) to assess R-loop levels.
• Genome-wide analyses to map R-loop alterations and APOBEC3B binding sites.
• Mutagenesis studies to examine the impact of APOBEC3B on gene mutation patterns.

Main Results:

• Proteomics identified numerous R-loop factors interacting with APOBEC3B.
• APOBEC3B directly binds to R-loops in cellular and in vitro settings.
• APOBEC3B deficiency increases R-loop accumulation, while overexpression decreases it.
• Genome-wide analyses revealed widespread alterations in R-loop landscapes and APOBEC3B binding.
• APOBEC3B mutagenesis preferentially affects genes in tumors, particularly those with splice factor mutations, and kataegis show APOBEC3B deamination motifs.

Conclusions:

• APOBEC3B plays a significant role in regulating R-loop formation and stability.
• The interaction between APOBEC3B and R-loops contributes to R-loop-associated mutagenesis in cancer.
• These findings reveal a novel mechanism linking APOBEC3B activity to cancer development through R-loop modulation.