Fig. 3: CG and non-CG methylation jointly repress TE activation and movement. | Nature Communications

Fig. 3: CG and non-CG methylation jointly repress TE activation and movement.

From: DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development

Fig. 3

a Number of differentially expressed TEs (DETs) in the indicated mutants relative to WT. b Venn diagram showing the overlap among up-regulated TEs in ddcc, met1-9, and mddcc mutants. c Heat maps showing the expression and DNA methylation patterns of TEs in the indicated groups. Based on the expression patterns of TEs, TEs were classified into the following categories: Redundancy, Dosage I, Dosage II, and Dosage III (for details, see Fig. 2e). d–f Circle plots showing TE transposition in different mddcc individual plants. Arrows start and end represent the original and inserted sites of transposed TEs, respectively. The red/green/blue arrows indicate that the transposed TE belongs to the ATCOPIA21, ATENSPM3, or VANDAL21 subfamily, respectively. g–i Products of PCR amplification with paired primers flanking new insertion sites or a transposon-specific primer and a primer flanking the new insertion site in the indicated genotypes. Black arrows indicate primers. Upper panels: screenshots from Integrative Genomic Viewer (IGV) showing split-reads for TE insertions. Lower panels, coordinate lines indicate the sequence contexts of the new insertion sites. j Snapshots of expression and DNA methylation levels over transposed TEs in the indicated mutants. Source data are provided as a Source Data file.

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