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. 2019 Feb 21;20:41. doi: 10.1186/s13059-019-1652-0

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — H3K27me3, H3K9me2, and CHG methylation overlap on maternal alleles of PEGs in crosses Col × Ler. a Overlap of genes marked by H3K27me3 and H3K9me2 on the maternal alleles. Dark red inset marks genes that have H3K27me3 and H3K9me2 exclusively on their maternal alleles (excluding genes also marked on the paternal alleles). b Genes marked by H3K27me3 and H3K9me2 have higher levels of H3K27me3. Box plots show mean values of z-scored H3K27me3 and H3K9me2 of genes where the maternal alleles are either marked by H3K27me3 alone or by a combination of H3K27me3 and H3K9me2. Genes containing maternal-specific H3K27me3 and H3K9me2 are particularly enriched for H3K27me3. Boxes show medians and the interquartile range, error bars show the full range excluding outliers. Notches show the 95% confidence interval for the median. Asterisks mark significance (Wilcoxon rank sum test, P < 1.0e−3). Presence of the mark corresponds to the mark highest score defined in Additional file 2: Table S1. c The majority of PEGs are marked by H3K27me3 and H3K9me2 on their maternal alleles. Overlap of PEGs [14] with maternal and paternal H3K27me3 and H3K9me2. d Levels of H3K27me3 and H3K9me2 on PEGs, MEGs, and all genes. Box plots (as specified in panel B) show mean values of z-scored H3K27me3 and H3K9me2. Asterisks mark significance (Wilcoxon rank sum test, P < 1.0e−3). e Metagene plots showing average distribution of z-score normalized H3K27me3 and H3K9me2 levels on maternal and paternal alleles of PEGs [14]. f Levels of DNA methylation in each sequence context (mCG, mCHG, and mCHH) on PEGs, MEGs, and all genes. Box plots (as specified in panel B) show mean values of relative DNA methylation. Asterisks mark significance (Wilcoxon rank sum test, P < 5.0e−3). Data shown correspond to cross Col × Ler [8], for reciprocal cross direction see Additional file 1: Figure S1