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The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

ABSTRACT: Purpose: This study seeks to determine whether GLI3 is required to recruit the SMARCC1 complex to GLI enhancers in the limb. Methods: To determine if Gli3 is required to recruit SMARCC1 to its anhancers, we performed differential chromatin binding to compare SMARCC1 binding in control and Gli3 mutants. We performed Cut&Run for SMARCC1 binding on individually genotyped E11.5 (40-43s) anterior forelimb pairs from control (Gli3+/+; 3 replicates) and Gli3 mutant (Gli3-/-; 4 replicates) embryos. Results: We found that there is no major difference in SMARCC1 binding in Gli3-mutants compared to controls.

ORGANISM(S): Mus musculus

PROVIDER: GSE224508 | GEO | 2024/02/03

REPOSITORIES: GEO

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The BAF complex does not mediate GLI repression (ATAC-Seq)

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

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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.

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Project description:Purpose: The response to Hedgehog signaling in the limb is driven by GLI bound enhancers and the majority of Hh targets in the developing limb bud are regulated solely by the activity of GLI-repressor. Currently we do not have a comprehensive understanding of how GLI bound enhancers respond Hedgehog signaling. The goal of this study is to identify how GLI bound enhancers are regulated by Hedgehog signaling and specifically by GLI-repressor. Methods: ChIP-seq was performed in Embryonic day 10.5 mouse limb buds from mice with endogenously FLAG tagged Gli3. Results: We identified 7282 GLI3 binding regions in the E10.5 limb bud.

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