Fig. 2: Low-CG promoter, long-first-exon or long intronless gene, and high histone acylation correlate with the production of pachytene piRNAs. | Nature Communications

Fig. 2: Low-CG promoter, long-first-exon or long intronless gene, and high histone acylation correlate with the production of pachytene piRNAs.

From: Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes

Fig. 2

a Bar plot reports the Spearman correlation coefficient between piRNA abundance and first exon length and promoter O/E CG, H3K4me3, H3K27me3, H3K4me2, H3K27ac, H4K5ac, H4K5bu, H4K8ac, H4K8bu, pan-lysine acetylation (Kac), pan-lysine crotonylation (Kcro), chromatin accessibility measured by ATAC-seq, DNA methylation, and RNA pol II binding at the promoters (TSS ± 2 kb) of pachytene piRNA clusters in pachytene spermatocytes. Significant correlations (Benjamin-adjusted p values < 0.05; n = 100) are marked in black, while nonsignificant correlations are marked in grey. b Histograms of first exon length of intronless pachytene piRNA clusters and the first exons of intron-containing pachytene piRNA clusters, pre-pachytene piRNA clusters, hybrid piRNA clusters, all protein-coding genes, and all lncRNAs. c The percentages of low-CG, intermediate-CG, and high-CG promoters. Eight groups are shown: pachytene piRNA clusters, pre-pachytene piRNA clusters, hybrid piRNA clusters, piRNA pathway genes, A-MYB-regulated protein-coding genes, A-MYB-regulated lncRNA genes, testis-specific protein-coding genes, and testis-specific lncRNA genes. d. Boxplots and meta-gene plots show histone modifications, ATAC, and RNA pol II levels at 100 pachytene piRNA clusters, 84 pre-pachytene piRNA clusters, 30 hybrid piRNA clusters, 17 piRNA pathway genes, 789 A-MYB-regulated protein-coding genes, 46 A-MYB-regulated lncRNAs, 1171 testis-specific protein-coding genes, and 164 testis-specific lncRNAs in pachytene spermatocytes. The x-axis for the box and the y-axis for the meta-gene plots report log2 ChIP signal or ATAC-seq read coverage relative to input, using a pseudo-count of 1. Asterisks indicate statistical significance (two-sided Wilcoxon rank-sum test p value < 0.001) for pairwise comparisons between 100 pachytene piRNA clusters and each of the other gene types. Red (blue) indicates that the epigenetic level is significantly higher (lower) in pachytene piRNA clusters. For boxplots, whiskers show 95% confidence intervals, boxes represent the first and third quartiles, and the vertical midline is the median.

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