Hijacking the transcriptional potential of the BAF complex for therapeutic purposes via induce proximity

The BAF (Brg/Brahma-associated factors) complex, also referred to as the mammalian Switch/Sucrose-Nonfermentable (mSWI/SNF) chromatin remodeling complex, plays a pivotal role in epigenetically regulating diverse transcriptional programs. BAF's chromatin remodeling activity, which enhances accessibility to transcriptional machinery, is critical for gene regulation. We hypothesize that redirecting endogenous BAF complexes to “turn on” therapeutically relevant genes offer an additional approach for disease treatment. Using chronic myelogenous leukemia K562 cells stably expressing the FIRE-dCas9 system (K562-FIRE) and rapamycin as a chemical inducer of proximity (CIP) via CRISPR/Cas9 and FKBP/FRB dimerization, we redirected endogenous BAF complexes to the promoter of fetal hemoglobin (HBG) using pooled small guide RNAs (sgRNAs) targeting the HBG1 promoter. RNA-seq analysis showed a statistically significant increase in HBG1 and HBG2 gene expression in rapamycin treated cells over the DMSO treated controls. Overall design: K562 cells stably expressing the FIRE-dCas9 system (K562-FIRE) were profiled via RNA-seq to test whether endogenous BAF could activate expression of HBG1 gene expression using sgRNAs targeting the HBG1 promoter (sgHGB1) or non-targeting sgRNAs (sgNT) after 24 h of 10 nM rapamycin or DMSO treatment.