The molecular basis of selective DNA binding by the BRG1 AT-hook and bromodomain

Area of Science:

• Molecular Biology
• Chromatin Biology
• Cancer Genomics

Background:

• The ATP-dependent BAF chromatin remodeling complex regulates gene expression by altering chromatin structure.
• BAF complex subunits are frequently mutated in over 20% of human cancers, highlighting its role in tumorigenesis.
• The precise mechanisms by which BAF navigates chromatin, involving multivalent histone and DNA interactions, remain incompletely understood.

Purpose of the Study:

• To investigate the DNA binding specificity of a composite domain within the BRG1 ATPase subunit.
• To elucidate the structural basis of DNA binding by this domain using biophysical and computational methods.
• To determine how cancer-associated mutations within this domain affect its DNA binding properties.

Main Methods:

• Systematic Evolution of Ligands by Exponential Enrichment coupled with Sequencing (SELEX-seq) to determine DNA binding preferences.
• Nuclear Magnetic Resonance (NMR) spectroscopy to analyze the structure and dynamics of the BRG1 domain.
• Molecular modeling to visualize the DNA-binding pocket and simulate the effects of mutations.

Main Results:

• SELEX-seq identified specific DNA sequence preferences for the BRG1 composite domain.
• NMR and modeling revealed the structural underpinnings of the domain's multivalent DNA association.
• Cancer mutations within the mapped DNA binding pocket were shown to alter the mode of DNA binding.

Conclusions:

• The BRG1 composite domain possesses specific DNA binding capabilities crucial for BAF complex function.
• Cancer mutations disrupt the normal DNA association mechanism of this critical domain.
• Understanding these structural and functional alterations provides insights into BAF-related cancers.