Extended Data Fig. 6: RNA degradation and genomic position dependent LTR-chimera biogenesis.
a, Bar plot displaying proportion of top 16 TE elements with SD-PAS found in Fig. 4a that were defined as TE-promoters. b, Pie charts displaying the percentage of all chimeric and non-chimeric LTR, grouped by the genomic position relative to the mm10 Ensembl transcriptome using ChIPseeker75,76 R package: promoter (3 kb around TSS), intragenic, downstream (of gene end) <= 300 bp, and distal intergenic. c, Box plot displaying average promoter-proximal antisense coverage from nascent RNA sequencing (metabolic labeling) between genes and its nearest promoter-proximal upstream intergenic LTR in WT, grouped by chimeric status (n = 11,532 non-chimeric and 60 chimeric). The box hinges represent the 25th and 75th percentiles, and the middle line represents the median. Whiskers extend from the hinges to the most extreme values within 1.5 times the inter-quartile range. Data beyond these limits are outliers. Asterisks and p-values were calculated based on an unpaired, two-sided Wilcoxon rank-sum test (p = 5.034297e-07). d, Density plot displaying log2 fold changes of average promoter-proximal antisense coverage from nascent RNA sequencing between gene and its nearest promoter-proximal upstream intergenic LTR in Exosc3 cKO compared to WT, grouped by chimeric status. P-values were calculated by an unpaired, two-sided Wilcoxon rank-sum test.
