Fig. 3: Direct binding of DUX4 to the HSV-1 genome.
From: Herpesviruses mimic zygotic genome activation to promote viral replication
A CUT&RUN with a DUX4-specific antibody in HFF1 cells infected with HSV-1 at 12 hpi performed in duplicates. One sample with an H3K27me3-specific antibody was included as control. Data was normalized to Drosophila Spike-in DNA. Lines labeled with KOS indicate the DUX4 motif sites in the HSV-1 genome determined with FIMO. B Comparison of DUX4 consensus binding sequence from DUX4 CUT&Tag in HSV-1 infected cells (upper panel), DUX4 HSV-1 ChIP-Seq (middle panel) and with the previously published DUX4 consensus sequences (Geng et al.) in the lower panel. C, D Electrophoretic Mobility Shift Assay (EMSA) of different 600 bp fragments of fluorescently labelled viral DNA containing either one DUX4 binding motif (B1/B2) or no DUX4 binding motif (NB), incubated with purified DUX4 protein (DUX4). B1 shows a T- > C nucleotide exchange at position 9 of the DUX4 binding motif in the KOS strain. Representative experiment out of n = 4. E Reanalysis of ATAC-seq and histone modifications at known DUX4 binding sites of THP-1 cells infected with HSV-1 at 1 h, 2 h, 4 h and 8 h post infection. Histone modification and ATAC-seq were taken from Gao et al. and Hennig et al. respectively33,34 and DUX4 binding sites from the DUX4 ChIP-Sequencing after HSV-1 infection. F Venn diagram showing overlap of genes that are significantly upregulated in the 8-cell stage of human development, HSV-1 infection and FSHD. G Expression pattern of embryonic genes during embryonic genome activation compared to expression pattern in DUX4 overexpressing and HSV-1 infected cells. Embryonic data is normalized to the average expression value of each gene. Data from DUX4 overexpression and HSV-1 infection is relative to mock. Shown are genes which have DUX4 binding sites in the proximity of the TSS (500 bp downstream, 1000 bp upstream of the annotated promoter). (OO: oozyte, PRO: pronucleus, ZY: zygote, 2 C: 2-cell state, 4 C: 4-cell state, 8 C: 8-cell state, MO: morula). Source Data are provided as a Source Data file.
