Enrichment of DNA methylation and H3K9me2 over transposable elements.

(A–B) Relative distance line plots of DNA methylation over transposable elements in maize and Arabidopsis. The plot in A shows the average enrichment for each type of DNA methylation of DNA transposons containing terminal inverted repeats (TIRs). The colors of the lines indicate the context of DNA methylation (black-CG; red-CHG; green-CHH) and type of line indicates the species (solid = maize; dashed = Arabidopsis). In (B) similar plots are shown for long terminal repeat (LTR) retrotransposons. (C) Plots of H3K9me2 abundance are shown for DNA transposons (purple) and retrotransposons (blue) in both maize (solid lines) and Arabidopsis (dashed lines). (D) The average level of DNA methylation or H3K9me2 is plotted for different sub-classes of transposable elements. The retrotransposons are divided into LINEs, RLG (gypsy-like), RLC (copia-like) and RLX (LTR elements of unknown class). The RLG, RLC and RLX elements are all split according to whether they exhibit evidence for spreading of H3K9me2 or DNA methylation in flanking regions as defined in Eichten et al [27]. The DNA transposons are divided into five major families (DTA (hAT), DTC (CACTA), DTH (PIF/Harbinger), DTM (Mutator) and DTT (Tc1/Mariner)) and for two of these there are large families of “non-coding” elements that are indicated as “-nc”. The last three bars indicate the average levels for each modification 1 kb away from TEs, within exons or within introns. (E) The relative levels of H3K9me2 and CHH methylation are shown for each sub-family of transposons. The levels for TE flanking regions, exons and introns are also shown.