6926 Nucleic Acids Research, 2011, Vol. 39, No. 16 Figure 5. Relationships between DNA methylation, size, CpG content and divergence of TE sequences. Color code is as in Figure 4. (a) Unmethylated TE sequences tend to be smaller than their methylated counterparts. (b) Boxplots showing observed versus expected CpGs for the three DNA methylation patterns considered. Unmethylated TE sequences are depleted in CpGs compared to poorly methylated TEs (P-value = 0.004793, Wilcoxon rank-sum test) or methylated TEs (P-value < 1 e 10). Poorly methylated TE sequences also have a lower CG content compared to methylated TE sequences (P-value = 5.369 e 13). (c and d) Average methylation levels of TE sequences are plotted according to length or percentage of identity with the TE reference sequence. Signiﬁcant positive correlation (black curve) is observed in each case. Table 2. TE sequences within genes Methylation Number Percentage Intronic Exonic Percentage Percentage pattern of TEs pattern intronic exonic UUU MMM UUM UMU MUU MUM MMU UMM 456 249 105 64 54 48 41 30 0.44 0.24 0.10 0.06 0.05 0.05 0.04 0.03 116 59 22 11 12 11 10 5 336 189 82 53 42 37 31 25 0.26 0.24 0.21 0.17 0.22 0.23 0.24 0.17 0.74 0.76 0.79 0.83 0.78 0.77 0.76 0.83 each half and its corresponding siRNA-associated ﬂank. As shown in Figure 6c, median DNA methylation densities are uniformly high along the 1 kb ﬂanks, but decrease progressively within the ﬁrst 500 bp of TE se- quences with no matching siRNAs. Correspondingly, the 5371 siRNA-associated MMM TE sequences show higher DNA methylation than their ﬂanks, which may or may not have matching siRNAs (Figure 6d). Taken together, these ﬁndings provide strong evidence that DNA methylation can spread over short distances ( 500 bp) from siRNA-targeted regions into ﬂanking sequences. Furthermore, analysis of additional methyl- omes (6) reveals that DNA methylation gradients are abolished in plants defective for the CG maintenance methyltransferase MET1 but are still detectable in plants