The associations between H3K9me3 density of genes and their neighborhood TE content.

<p>(A) Boxplots for the H3K9me3 density of genes that are of different distance from TEs. The H3K9me3 density of genes that have at least one TE in the introns of the gene (in gene), within 1kb, 1-2kb, 2-5kb, and 5-10kb upstream/downstream from the gene are significantly lower than those of genes that have no TE 10kb upstream/downstream (whose median of H3K9me3 density is shown as a dashed line). Numbers of genes in each category are 588 (in gene), 579 (within 1kb), 323 (1-2kb), 859 (2-5kb), 1162 (5-10kb), and 8072 (no TE in 10kb). All comparisons are against genes without TEs in 10kb upsteam/downstream. Result of 0–4 hr embryo is shown. (B) The <i>spearman rank</i> correlation coefficients between H3K9me3 density of a gene and the number of adjacent TEs within a specific window decrease as the distance between genes and TEs increases. The median, mean, and maximum number of TEs in specific windows are (1) in gene: 0 (median), 0.0523 (mean) and 8 (maximum), (2) 0-1kb: 0 (median), 0.0555 (mean), and 4 (maximum), (3) 1-2kb: 0 (median), 0.0341 (mean), 2 (maximum), (4) 2-5kb: 0 (median), 0.101 (mean), and 5 (maximum), and (5) 5-10kb: 0 (median), 0.158 (mean), and 7 (maximum). Notations for <i>p-values</i> are * (<i>p</i> < 0.05), ** (<i>p</i> < 0.01), and *** (<i>p</i> < 0.001).