Fig. 3: HNF1A–BAF complex binding cooperates with high motif density at the ACE2 locus to regulate ACE2 expression.
From: Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection
a, Transcription factor motif enrichment analysis at BAF-gained sites (cluster 3). b, Transcription factor motif enrichment at BAF-occupied gained sites after rescue of Vero E6 SMARCA4 knockout cells with WT SMARCA4 plotted against log2 fold change of the transcript levels of the transcription factors (empty vector versus WT SMARCA4 conditions). HNF1A and HNF1B are circled in red. c, Immunoblot of HNF1A/B across WT Vero E6 and SMARCA4 knockout cells rescued with empty vector, WT SMARCA4 or SMARCA4 K785R. d, ACE2 expression in HNF1A and HNF1B knockout Vero E6 cells measured by RT–qPCR (left) and immunoblot (right). e, WT and HNF1A/B knockout Vero E6 cells were infected with icSARS-CoV-2-mNG at an MOI of 1. The frequency of infected cells was measured using mNeonGreen expression 2 d after infection. f, Vero E6 cells were infected with SARS-CoV-2 at an MOI of 0.1. Virus production was measured by plaque assays. g, HNF1A and HNF1B knockout Vero E6 cells were infected with SARS-CoV-2 pseudovirus. Luciferase relative to VSVpp-VSV-G control was measured 1 d after infection. h, Coimmunoprecipitation of endogenous SMARCA4 and HNF1A in nuclear extracts isolated from Vero E6 cells. i, HNF1 dimerization and association studies in WT and SMARCA2/4 double-knockout HEK 293T cells. j, Heatmap of SMARCA4 and SMARCC1 merged C&T (n = 1) and ATAC–seq (n = 2) peaks in control and HNF1A knockout Vero E6 cells, divided into three clusters. k, Bar graph depicting the fraction of sites with an HNF1 motif near cluster A (lost sites), cluster B (gained sites) and cluster C (unchanged sites) from j. l, Normalized gene rank of genes closest to cluster A sites plotted against the number of HNF1 motifs per gene at cluster A sites; selected genes within the top 10% of sites regulated by HNF1A are shown. m, C&T and ATAC–seq tracks at the ACE2 locus in control and HNF1A knockout Vero E6 cells. The data in c, d, h and i are representative of one of three independent experiments. The data in d–g were analyzed using a one-way ANOVA with Tukey’s multiple comparisons test. The mean ± s.e.m. are shown. ***P < 0.001, n = 3 biological replicates.
