Heterochromatin spreading is restricted to some retrotransposon families.

<p>The 144 families of class I retrotransposons represented by at least 1000 probes within the adjacent 4 kb were identified and the average level of H3K9me2, 5-methylcytosine and K3K27me3 enrichment was determined for 200 bp bins. The average values are calculated from both sides of annotated elements collapsed. (A) The relative level of DNA methylation in each 200 bp bin is shown for each of the 144 families. The red color indicates enrichment for the modification while blue indicates depletion of the mark. Black indicates levels of the modification similar to genome-wide average values. The color intensity is based on the average log ratio of immunoprecipitated DNA relative to input DNA. The retrotransposons are grouped according to whether they show spreading for DNA methylation and H3K9me2, H3K9me2 only or neither of the marks. Similar plots are shown for H3K9me2 (B) and H3K27me3 (C). (D) Whole-genome bisulphite sequencing data was used to assess the methylation level in different cytosine contexts in the low-copy (based on the absence of repetitive sequences) 1 kilobase regions flanking spreading (both), spreading (H3K9), non-spreading retrotransposons and for 10,000 random genomic regions. The error bars indicate standard deviation among retrotransposon families and “*” indicate significant (p<0.001) differences for a group relative to the non-spreading families. The level of CG and CHG methylation is higher for spreading retrotransposons than for non-spreading retrotransposons. (E–H) show plots of representative family(s) for each class. The relative abundance of DNA methylation (black), H3K9me2 (blue) and H3K27me3 (green) is shown for the first 3 kb of low-copy DNA flanking the retrotransposon family on both sides. The y-axis indicates enrichment relative to genome-wide average (value of 0 is equal to average of permuted data).