PBRM1 bromodomains variably influence nucleosome interactions and cellular function

Area of Science:

• Molecular Biology
• Epigenetics
• Cancer Research

Background:

• Chromatin remodelers utilize bromodomains (BDs) for histone recognition.
• Polybromo 1 (PBRM1), a component of the PBAF chromatin-remodeling complex, is frequently mutated in clear cell renal cell carcinoma (ccRCC).
• Individual PBRM1 BD binding specificities have been explored, but the influence of neighboring BDs on nucleosome recognition remains unclear.

Purpose of the Study:

• To investigate the histone-binding characteristics of individual and combined PBRM1 bromodomains.
• To determine how neighboring bromodomains influence PBRM1's nucleosome interactions.
• To analyze the impact of ccRCC-associated mutations in PBRM1 on chromatin interactions and ccRCC cell proliferation.

Main Methods:

• Histone microarrays and intact nucleosome assays were employed to study PBRM1 BD binding.
• Biochemical and mutational analyses were performed on full-length PBRM1 and its domains.
• ccRCC cell proliferation assays were conducted to assess the functional impact of mutations.

Main Results:

• PBRM1 BD2 and BD4 mediate binding to acetylated histone peptides and modified nucleosomes.
• Neighboring BDs (BD1, BD5, BD3) variably modulate the nucleosome binding of BD2 and BD4.
• ccRCC-associated missense mutations in PBRM1 BD4 disrupt chromatin interactions and accelerate ccRCC cell proliferation.

Conclusions:

• PBRM1 BD4 is critical for proper PBRM1 function in chromatin regulation.
• Mutations in PBRM1 BD4 enhance ccRCC cell growth, highlighting its oncogenic role.
• PBRM1 BD4 mutations may represent a potential clinical target, given the link between PBRM1 and immune checkpoint inhibitor sensitivity.