Fig. 1: Mouse pachytene piRNA clusters show testis-specific expression and epigenetic signals.
a Each column represents a piRNA gene, grouped by type (pachytene, hybrid, and pre-pachytene) and sorted by tissue-specificity score (“Methods”) within each group. Each piRNA gene is further annotated by its function as an mRNA (black/grey), low, intermediate, or high-CG level at the promoter (low-CG, intermediate-CG, or high-CG; in blue, green, and yellow), length of first exon or length of intronless gene (≥10 or <10 kb; in red and pink), piRNA abundance (RPM) in adult testis, and transcript expression level (RPKM) in the testis, eight somatic tissues, and fetal ovary. piRNA abundance and transcript expression levels are log2 and log10 transformed, respectively, with a pseudo-count of 1 and share the same color scale. b Each panel indicates the levels of RNA pol II binding or a histone mark; tissues are color coded. Pachytene piRNA clusters exhibit high levels of activating histone marks (H3K4me3, H3K4me2, H3K4me1, H3K27ac, and H3K36me3), low levels of the repressive histone mark H3K27me3, and high levels of RNA pol II binding specifically in adult testis. ChIP-seq signals are shown in a ±2 kb window around the TSS in 10 bp bins. H3K4me2 ChIP-seq data were publicly available only for testis, liver, and brain. We performed two-sided Wilcoxon signed-rank tests to compare epigenetic signals at pachytene piRNA clusters in the testis versus somatic tissues. Pol II, p < 2.2 × 10−16; H3K4me1, 2.3 × 10−16 < p < 6.9 × 10−16; H3K4me2, 1.0 × 10−11 < p < 3.0 × 10−10; H3K4me3, p < 2.2 × 10−16; H3K27ac, p < 2.2 × 10−16; H3K27me3, 2.3 × 10−11 < p < 7.9 × 10−6; H3K36me3, 1.7 × 10−16 < p < 2.4 × 10−16.
