(A, C) Boxplots of H3K9me2, CHG methylation (mCHG), and sRNA expression changes in h1 vs. wt (A) and h1c2c3 vs. c2c3 (C). (B, D) Correlation among H3K9 methylation, DNA methylation, and sRNA expression in h1 plants (B) and h1c2c3 plants (D). (E, F) sRNA expression relation to H3K9me1, CG, and non-CG methylation density in h1 plants (E) and h1c2c3 plants (F). Each dot represents the average of 100 transposable elements (TEs) sorted by GC content. DNA methylation density equals number of methylated sites per base pair. (G) Average sRNA expression level of chromomethylase (CMT) TEs in wt, h1, c2c3, and h1c2c3 plants. (H) Example of DNA methylation, sRNA expression, H3K9 methylation (K9me1 and K9me2), and H1.1 distribution at CMT TEs in wt, h1, and h1c2c3 plants (Chr2: 6,548,000–6,559,000).