Project description:Purpose: This study seeks to determine whether Smarcc1 mediates GLI repression through chromatin compaction in the limb. Methods: To determine if Smarcc1 mediated GLI repression through chormatin compaction, we used genomic approached to determine changes in chromatin accessibility in control and Smarcc1-conditional mutants. We performed ATAC-seq on individually genotyped anterior forelimbs at E11.5 (40-48s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (3 replicates) embryos. From this experiment we identified ~10,000 differentially accessible regions (FDR<0.05). Results: We find that SMARCC1 is required to maintain chromatin accessibility at thousands of regions within the mouse limb, including most HH-responsive GLI enhancers
Project description:Purpose: This study seeks to determine whether Smarcc1 co-regulates Hedgehog (HH) target genes in the limb. Methods: To determine if Smarcc1 is required to regulate HH targets, we used genomic approaches to identify Smarcc1-regulated genes within the forelimb. We performed bulk RNA-seq on individually genotyped forelimb-bud pairs at E11.5 (39-40s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos. From this experiment we identified 928 differentially expressed genes (FDR<0.05). Results: We find that while certain HH target genes are co-regulated by SMARCC1, the majority of HH target genes do not require Smarcc1.
Project description: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.
