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. 2022 Jul 1;34(10):3685–3701. doi: 10.1093/plcell/koac199

Figure 5.

Figure 5

A, Genes that overlap endosperm DMRs are skewed toward maternal expression but are still predominantly biallelically expressed. A value of 1 means completely maternal expression and 0 means completely paternal (Anderson et al., 2021). Genes are categorized according to distance from endosperm DMRs. Numbers of genes in each category are indicated. B, MEGs preferentially overlap endosperm DMRs. Genes are categorized according to distance to the closest DMR (by color) and according to imprinting status (X-axis labels, including total number of genes in each imprinting category). MEGs are defined by a maternal ratio of greater than 0.9, PEGs as less than 0.1, biallelic as intermediate values. Only genes with SNPs and sufficient coverage to make imprinting calls are included. Significant differences between imprinted and biallelic sets are indicated by “S.” (P < 0.00001, two-tailed chi-square test), or “s.” (P < 0.01, two-tailed chi-square test). The larger proportions for endosperm vs. embryo are because of the larger number of DMRs (52,191, compared to 18,464 in WT vs. mdr1 endosperm. C, Endosperm gene expression is not correlated with DMRs. Genes are categorized according to distance to the closest DMR (by color) and according to expression status (X-axis labels, including total number of genes in each expression category). “Endosperm on” means expressed in endosperm, “endosperm off” means not expressed in endosperm but expressed in other tissues, and “constitutive off” means not expressed in endosperm and not expressed in other tissues. Data from Stelpflug et al. (2016). No differences between endosperm on and off categories were significant (P > 0.01, two-tailed chi-square test. D, MEGs are enriched for endosperm DMRs near their 5′ ends. DMR enrichment is the number of DMRs that overlap with a 1-kb range either centered on transcription start sites (TSS) or polyadenylation sites (polyA) of MEGs normalized by the number of control regions that overlap the same range. E, Maternal imprinted transposons have a high frequency of overlap with endosperm DMRs. MEG-type transposons (95 total) have a maternal ratio value greater than 0.9, PEG as less than 0.1, and non-imprinted (1,773 total) as all intermediate values. The Y-axis indicates the proportion of transposons that overlap endosperm DMRs from each of the two comparisons. In both, MEG-type transposons are significantly enriched for DMRs over non-imprinted ones (P < 0.01, binomial test). Only one PEG-type transposon overlapped with DMRs and is not shown.