Section 3: BAF Function in Transcription and Accessibility

What technique is used to measure chromatin accessibility and nucleosome organization genome-wide?

ATAC-seq (Assay for Transposase Accessible Chromatin).

Why is reduced nucleosome density at a gene's transcription start site (TSS) important for transcription?

It allows transcription factors to bind to the DNA and initiate transcription.

What is the primary mechanism by which the BAF complex activates transcription?

It uses ATP to remodel chromatin, increasing accessibility at promoters and enhancers, thereby facilitating the binding of transcription factors and evicting repressor complexes.

How does the BAF complex oppose Polycomb repressor function?

Studies show that artificially recruiting BAF to a gene leads to rapid increased accessibility and eviction of Polycomb repressors and their associated repressive histone modifications, leading to gene activation.

What happens to chromatin accessibility when the catalytic SMARCA4 subunit is knocked out or inhibited?

There is a rapid loss of chromatin accessibility, tightly coupled to the loss of lineage-specific transcription factor binding.

What is the role of BAF in cell fate decisions?

BAF is a critical player in cell fate decisions and differentiation by establishing the correct chromatin landscape for gene expression progra