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. 2015 Jul 5;168(4):1417–1432. doi: 10.1104/pp.15.00414

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Figure 4. — Dynamic DNA methylation of rice embryo and endosperm. A, Number of regions with differential DNA methylation. Increased or decreased DNA methylation between consecutive stages during embryo and endosperm development is shown. For the detection of differential methylation regions, see “Materials and Methods.” B, Distribution of differentially methylated regions in relation to gene annotation between consecutive developmental stages, which is compared with the average proportion of methylated region distribution for embryo and endosperm. Genomic regions were divided into five categories: proximal promoter (1 kb upstream of the TSS), exon, intron, transcriptional termination region (1 kb downstream of the TES), and intergenic region. Student’s t test was performed and revealed significantly more exonic regions for differentially methylated loci compared with all methylated loci in embryo (P = 0.0397), while no significant difference was detected in endosperm (P = 0.62). C, Cumulative distribution of the coefficient of variance in log₂ scale for DNA-TEs, LINEs, LTRs, SINEs, and non-TE genes. The K-S test was performed and revealed a significant difference between non-TE genes and TEs, LTRs, and other TEs or non-TE genes (P < 0.001). D, DNA methylation level negatively correlates with the gene expression level in rice embryo and endosperm. The expression intensity in log₂ scale of all examined genes was sorted in ascending order (left), and the methylation intensity around the TSS (middle; from 3 kb upstream of the TSS to 3 kb downstream of the TSS) and the TES (right; from 3 kb upstream of the TES to 3 kb downstream of the TES) of the corresponding genes was plotted. The methylation intensity around the TSS and TES is generated from the average read density normalized by sequencing depth and window size of 20 bp (RPKM). Each row in the heat map of expression represents a gene, and each column in the heat map of methylation intensity corresponds to the RPKM in each 20-bp bin around the TSS (middle) or the TES (right). The expression and methylation patterns of embryo or endosperm at 3 DAP are shown, and all other samples have the same pattern.