Nucleic Acids Research, 2011, Vol. 39, No. 16 6927 Figure 6. Relationship between methylated TE sequences and 24-nt siRNAs. (a) Methylated euchromatic TE sequences are almost always associated with an abundance of siRNAs. (b) A signiﬁcant number of heterochromatic TE sequences are methylated but not associated with siRNAs (c) Methylated hetrochromatic TE sequences (size >200 bp) not associated with siRNAs but ﬂanked within 1 kb on one or both sides by sequences associated with siRNAs. These TE sequences were split in half and DNA methylation densities were calculated in 100-bp windows along the two ﬂanks and TE sequence halves by dividing the number of reads indicative of methylation at CG, CHG and CHH sites by the total number of cytosine-covering reads. Results are shown as boxplots of DNA methylation densities. Average normalized siRNA densities are also indicated for each 100-bp window. DNA methylation densities are uniform along the 1 kb ﬂanks, but decrease progressively within the ﬁrst 500 bp of TE sequences from both sides. (d) TE sequences associated with 24-nt siRNAs show increasing methylation from their extremities and decreasing methylation in their ﬂanks.