Extended Data Fig. 9: Decreased expression of PSG genes is associated with reduced intronic LTR8B chromatin accessibility. | Nature Cell Biology

Extended Data Fig. 9: Decreased expression of PSG genes is associated with reduced intronic LTR8B chromatin accessibility.

From: Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal–fetal interface following SARS-CoV-2 infection

Extended Data Fig. 9: Decreased expression of PSG genes is associated with reduced intronic LTR8B chromatin accessibility.

a, Peak-to-gene linkage analysis of PSG genes and their corresponding intronic LTR8B elements (red boxes). Tracks are displayed as pseudo-bulk signals of each cell type from the snATAC-seq and the colour scale represents the correlation value. b, Genome browser screenshot of the PSG gene cluster with expression and histone modifications tracks of TSCs. The blue shadings highlight the intronic LTR8B elements within PSG genes. All tracks are displayed as RPM, y axes are range from 0 to 2 for RNA-seq, 0 to 80 for H3K27ac, 0 to 40 for H3K4me1 and 0 to 80 for H3K4me3. c, Chromatin accessibility of LTR8B individual elements in all cell types from the snATAC-seq. Each dot represents an LTR8B element; P values were calculated using a one-tailed Wilcoxon test. Elements were filtered for RPKM > 1 in at least one cell type and length > 400 bp (n = 242). d, Chromatin accessibility of all LTR8B individual elements (left; n = 125) and LTR8B elements outside the PSG cluster (right; n = 114). Each dot represents an LTR8B element; P values were calculated using a one-tailed Wilcoxon test. LTR8B elements were filtered by RPKM > 1 in either control or patient sample and length > 400 bp. e, Genome browser screenshot of the STS gene promoter region. The blue shading highlights an LTR8B element. All pseudo-bulk tracks from the snRNA-seq, snATAC-seq and ChIP–seq tracks from the IHEC data repository are displayed in RPM. Significant interactions (one-tailed binomial test Padj < 0.05) predicted by Fit-Hi-C are displayed by purple arcs. The y axes are range from 0 to 15 for snRNA-seq, 0 to 6 for snATAC-seq, 0 to 200 for H3K27ac, 0 to 200 for H3K4me1 and 0 to 500 for H3K4me3. 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.

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