Extended Data Fig. 8: Downregulation of the expression of PSG genes due to SARS-CoV-2 infection during pregnancy.
a, Expression of PSG2 (top left), PSG3 (top right), PSG5 (middle left), PSG6 (middle right), PSG7 (bottom left) and PSG8 (bottom right) in the trophoblast cell types from the snRNA-seq calculated by Seurat. b, Expression of PSG genes from the bulk RNA-seq. Each dot represents a sample (n = 7 for both patient and control) and the Padj (two-tailed Wald test) was calculated by DESeq2. c, Chromatin accessibility signal of each intronic LTR8B within a PSG gene in the ST cell type from the snATAC-seq. d, Chromatin accessibility signal of intronic LTR8B elements within PSG genes in all nine cell types from the snATAC-seq. Each dot represents one LTR8B element (n = 11); P values were calculated using a one-tailed Wilcoxon test. e, Luciferase assay for promoter activity of individual intronic LTR8B elements within different PSG genes. Data are presented as mean values with error bars showing the s.d. and each dot representing an independent experiment (n = 3). f,g, Correlations between bulk RNA-seq expression levels of PSGs and the bulk ATAC-seq signals (f) as well as the H3K27ac CUT&Tag signals (g) of corresponding intronic LTR8B elements. The y axes represent the FPKM signal from the bulk RNA-seq and the x axes represent the RPKM signal from the respective assays. The error bands in grey represent a 95% confidence level interval for predictions from a linear model; Spearman’s correlation was used to calculate the R value. For all boxplots in this figure, the centre and bounds of boxes indicate the median and quartile of all data points, respectively. The minima and maxima of whiskers indicate quartile 1 − 1.5× the interquartile range and quartile 3 + 1.5× the interquartile range, respectively.
