Comparison of DNA methylation levels in the genic and TE regions among V0 (no vernalization), V4 (vernalized for 4 weeks), and V8 (vernalized for 8 weeks). A, Comparison of methylation levels in genic and TE bodies and their 2-kb flanking regions upstream (Up) and downstream (Down; Wilcoxon test, *P<0.05). B, Methylation profiles in genic and TE regions. The mean level for each 100-bp interval is plotted. “TSS” indicates the transcriptional start site, and “TTS” indicates the transcription termination sites. C, Methylation of TE Class I (retrotransposons) and Class II (DNA transposons) in the gene body and flanking 2-kb regions. “Body” indicates the insertion is in the gene body region, and “Flank” indicates the insertion is in the flanking 2-kb region (Wilcoxon test, *P<0.05). D, TE methylation level related to the distance from the closest gene; “0” indicates that the TEs are inserted into the gene bodies.