Extended Data Fig. 5: HNF1A directs BAF complex targeting and regulates ACE2 expression.
From: Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection
(a) RPKM levels for HNF1A and HNF1B in Vero E6 WT and SMARCA4 KO cells rescued with empty vector (Empty), SMARCA4 WT (A4 WT) or SMARCA4 K785R (A4 K785R) (n = 2 biological replicates). (b-c) ACE2 expression in HNF1A and HNF1B polyclonal KO Huh7.5 cells as measured by immunoblot (b) and RT-qPCR (c). (d) Huh7.5 cells were infected with icSARS-CoV-2-mNG at an MOI of 1. Infected cell frequency was measured by mNeonGreen expression at 2 dpi. (e) HNF1A and HNF1B polyclonal KO Huh7.5 cells were infected with VSV pseudovirus (VSVpp): VSVpp-VSV-G, VSVpp-SARS-CoV-2-S. Luciferase relative to the VSVpp-VSV-G control was measured 1 dpi. (f) Co-immunoprecipitation of SMARCA4 with HNF1A and HNF1B in HEK293T cells. (g) Co-immunoprecipitation of SMARCA4 with Flag-tagged HNF1A (F-HNF1A) in the presence of benzonase in HEK293T cells. (h) PCA plot of merged ATAC-Seq peaks in Vero E6 Control and HNF1A KO cells. (i) Scatter plots of ATAC-Seq replicates in Vero E6 Control and HNF1A KO cells. The correlation coefficient ‘r’ is indicated (top left). (j) Distance to TSS distribution of CUT&Tag and ATAC-Seq merged peaks for all conditions, across Clusters A-C in Vero E6 Control and HNF1A KO cells. (k) Heatmap depicting TF motif enrichment in Clusters A-C from Fig. 3j in Vero E6 Control and HNF1A KO cells. (l) Metaplots of SMARCA4, SMARCC1, H3K27ac and H3K4me1 chromatin occupancy (CUT&Tag) and DNA accessibility (ATAC-Seq) across Cluster A sites (lost sites) from Fig. 3j in Vero E6 Control and HNF1A KO cells. Data in (b, f-g) is one representative one of three independent experiments. Data in (c-e) were analyzed by one-way ANOVA with Tukey’s multiple comparison test. Shown are mean ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, n = 3 biological replicates.
