Extended Data Fig. 8: Dual-strand piRNA producing loci are associated with both H3K9me3 and H3K27me3 in Drosophilids.
a, Protein sequence alignment of the chromodomains of Rhi orthologs across the indicated species. Residues forming the hydrophobic pocket for trimethyl lysine binding are indicated in red. Residues important for chromodomain dimerization are indicated in green. b, Violin plots illustrating the distribution of piRNAs, H3K9me3 and H3K27me3 CUT&RUN signal [log10(rpkm+1)] in D. simulans, D. erecta, and D. ananassae ovaries. All 10 kb bins across the genome were divided into 15 groups. Group 1 contains all 10 kb bins with no piRNA expression. The 14 remaining groups contain an equal number of 10 kb bins. Groups are ranked according to piRNA expression levels with the lowest level of the two strands shown to focus on dual-strand regions. Boxplots show median (central line), interquartile range (IQR, box), and minimum and maximum values (whiskers, at most 1.5*IQR). c, Model of the Rhi chromodomain dimer in complex with a histone 3 peptide with trimethylated K9 and K27 residues. Representative frame obtained from 1 µS molecular dynamic simulations show the potential for the dimer’s interaction with both H3K9me3 and H3K27me3 to be simultaneous. Zoom-in indicated aromatic residues that interact with the methylated lysine group. d, UCSC genome browser tracks of D. melanogaster chromosome 4 displaying the binding profiles of the indicated chromodomain constructs measured by CUT&RUN (counts per million [cpm] across pooled replicates). Gene tracks are shown above.
