The BAF complex does not mediate GLI repression (WT Cut&RUN)

Purpose: This study seeks to identify SMARCC1-bound regions in the mouse limb. Methods: To identify SMARCC1 bound regions in the limb, we performed Cut&Run on pooled anterior and posterior wild-type forelimbs at E11.5 (43-44s; 3 replicates each) and on whole forelimb pairs at E9.5 (21-24s; 2 replicates). We identified 28,082 SMARCC1-bound regions in the anterior forelimb at E11.5, 42,530 regions in the E11.5 posterior limb, and 10,792 SMARCC1-bound regions at E9.5 (FDR<0.05). Results: We find that SMARCC1 is bound to most limb enhancer regions at late stages (E11.5). Additionally, We find that SMARCC1 is bound to the majority of HH-responsive GLI enhancers at E11.5 but only a small portion of GLI enhancers at E9.5. Overall design: Cut&Run E11.5 (43-44s; 3 replicates per condition) anterior and posterior forelimb buds, and E9.5 (21-24s; 2 replicates) forelimb buds from wild-type embryos.