Fig. 5: Silencing active TEs is a conserved function driving pachytene piRNA evolution.

a The percentage of active TE sequences and total TE sequences in piRNA loci (red) and in randomly shuffled control sequences (aquamarine). Human n = 88, and mouse n = 100. Violin plots represent 10,000 randomly shuffled control sequences. b Immunofluorescence labeling of mouse round spermatids. γH2AX, marker for double strand breaks. The foci numbers were quantified from 90 round spermatids from three biological replicates. Scale bar, 10 µm. c Scatter plot of mean TE transcript abundance in Mov10l1 CKO mutants versus that of littermate controls (n = 3). Each filled circle represents a TE family. Red, q value < 0.1. Each large circle represents an active TE family. Tpm transcript per million. d The 5′-5′ overlap between sense and anti-sense piRNAs mapping to TEs that are significantly increased in Mov10l1 CKO mutants. Data are mean ± standard deviation (n = 3). Ppm parts per million. e Scatter plot of mean TE transcript abundance in 19 chickens from the 6 breeds versus mean TE piRNA abundance in 23 chickens from the 6 breeds. 30 active TE families (red). Rpkm reads per kilobase pair per million reads mapped to the genome. p value was calculated by Spearman’s rank correlation coefficient statistical test. f Box plots of the distance between SV hotspots and nearest protein coding genes in (upper) humans (piRNA n = 88, SV minus piRNA n = 269) and in (lower) chicken macrochromosomes (piRNA n = 779, SV minus piRNA n = 26). We only calculated the distance on macrochromosomes including chromosome Z in chickens where most of the piRNA loci localized (751/1321) because the assembly of microchromosomes has not been completed. p value is smaller than the threshold we can compute. Box plots show the 25th and 75th percentiles, whiskers represent the 5th and 95th percentiles, and midlines show median values. g Example of a pachytene piRNA locus overlapping with 16 SVs deposited in ClinVar. From top to bottom: RefSeq, pathogenic SVs (each SV is labeled by its Variation ID, and Red is associated with autism spectrum disorder), and piRNA reads from adult human testes (Blue represents Watson strand mapping reads; Red represents Crick strand mapping reads).