Fig. 4

AGDP1 contributes to transcriptional silencing and non-CG methylation at some loci. a The transcript levels of the indicated TEs were determined by quantitative RT-PCR in the wild-type, agdp1-1, and agdp1-2. Error bars are SDs of three biological replicates. b The RNA transcripts of AtMU1, AtGP1, AtSN1, and ERT7 were detected by quantitative RT-PCR in the wild-type, agdp1-1, and agdp1-2. Error bars are SDs of three biological replicates. c The numbers of CG, CHG, and CHH hypo-DMRs and hyper-DMRs identified in agdp1-1. d The distribution of hypo-DMRs throughout the five chromosomes. Black, pink, and green bars represent CG, CHG, and CHH hypo-DMRs, respectively. Red circles indicate centromeres. e Composition of the genomic location of the hypo-DMRs. TE, transposable element. f Average DNA methylation levels along protein-coding genes (upper) and TEs (lower) and the 2-kb flanking regions in different cytosine contexts. Gray and pink curves represent DNA methylation levels of wild-type and agdp1-1, respectively