(A) Spearman rank correlation coefficients (ρ) between the magnitude (filled bars) and extent (open bars) of TE-mediated H3K9me2 enrichment and genic H3K9me2 enrichment level (top) and gene expression rank (higher rank means lower expression; bottom) of nearby genes. Most of the Spearman rank correlation coefficients are significantly different from 0 for comparisons of genic H3K9me2 enrichment level (top), but not for comparisons of gene expression rank (bottom). (B) Spearman rank correlation coefficients (ρ) between the magnitude (top) and extent (bottom) of TE-mediated H3K9me2 enrichment and the H3K9me2 enrichment level (left) and gene expression rank (right) of nearby genes for TEs 5’ (dark blue/orange) and 3’ (light blue/light orange) to genes. For the genic H3K9me2 enrichment, all Spearman rank correlation coefficients are significantly different from 0 except for one test. For gene expression rank, few correlations are significantly different from 0. (C) z-Scores for comparing the H3K9me2 enrichment (left) and expression rank (right) of homologous genic alleles whose nearby TEs with (blue/orange) or without (gray) epigenetic effects (as defined as the magnitude of H3K9me2 enrichment >1; see Figure 3—figure supplement 7 for categorizing TEs with the extent of H3K9me2 enrichment, which gives similar results). A positive z-score means the allele with TE has higher H3K9me2 enrichment or larger expression rank (i.e., lower expression level) than the homologous allele without TE in another strain. (D) A cartoon describing the ‘genic side’ and ‘intergenic side’ extent of H3K9me2 enrichment mediated by TEs is shown on the left. z-Scores for comparing the extent of TE-mediated H3K9me2 enrichment on the intergenic side and on the genic side for TEs close to (green) and far (gray) from genes whose expression is at least 10 RPKM. A positive z-score means that the extent of TE-mediated H3K9me2 enrichment is more restricted on the genic side than the intergenic side. In several genomes, z-scores for TEs close to genes are significantly different from 0 and/or larger than those for TEs distant to genes. mel: Drosophila melanogaster, mau: Drosophila mauritiana, sim1: Drosophila simulans strain 1, sim2: D. simulans strain 2, tei: Drosophila teissieri, san: Drosophila santomea, yak1: Drosophila yakuba strain 1, yak2: D. yakuba strain 2. ***p<0.001, **p<0.01, *p<0.05 for Spearman rank correlation tests (A, B) and Mann-Whitney U tests (C, D).