Fig. 8: Intronic LTR8B elements interact with PSG gene promoters.
a, Screenshot of the virtual 4C results (top) and Hi-C interaction frequency (bottom) from TSCs at the PSG cluster showing the interaction of PSG gene promoters and intronic LTR8B elements. The virtual 4C shows interaction frequencies using each intronic LTR8B element as an anchor. The intronic LTR8B elements and the promoters of PSG genes are highlighted with blue and yellow shading, respectively. The tracks are displayed as RPKM, with y axes ranging from 0 to 20,000. The white arrowheads in the Hi-C heatmap point to interactions within the PSG cluster, indicating a high interaction frequency between intronic LTR8B and the promoters of PSG genes. b, Pseudo-bulk RPKM signal of all active LTR8B elements defined by co-accessibility analysis (n = 83) in the nine cell types from the snATAC-seq. Each dot represents one active LTR8B element; P values were calculated using a one-tailed paired Student’s t-test. The centre and bounds of the 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. c, HOMER motif analysis of active LTR8B elements defined by the co-accessibility analysis (n = 83). P values were calculated using a one-tailed hypergeometric test. Ctrl, control and Cov, COVID-19; cell-type abbreviations as per Fig. 1b.
