Fig. 4: Characterization of MARs in Col-0.

a Heatmap showing the enrichment of DNaseI/input and MAR/input peaks in genic regions. b Metagene plots showing the MAR enrichment of Col-0 over genes (upper) and transposable elements (TEs, down). Genes are scaled to align their TSSs and TESs. Average enrichment means the percentage of regions (calculated from 100-bp windows) enriched for the respective epigenetic mark. TSS: transcription start site, TES: transcription end site. c Distribution of average epigenetic features across MARs over genes. Tri-methylation of histone H3 at lysine 4 (H3K4me3), tri-methylation of histone H3 at lysine 36 (H3K36me3), acetylation of histone H3 at lysine 9 (H3K9ac), acetylation of histone H3 at lysine 23 (H3K23ac), tri-methylation of histone H3 at lysine 27 (H3K27me3), mono-methylation of histone H3 at lysine 27 (H3K27me1), di-methylation of histone H3 at lysine 9 (H3K9me2), DNA methylation (DNAm), histone H3.1 (H3.1), histone H3.3 (H3.3), DNase-seq (DH), Pol2 ChIP-seq peaks (Pol2). d Box plot showing the expression level (reads per kilobase of exon per million reads mapped, RPKM) of non-MAR targeted (n = 21255) and MAR targeted (n = 7234) genes from RNA sequencing, N.S. p value > 0.05, *p value ≤ 0.05, **p value ≤  0.01, ***p value ≤ 0.001. (Kolmogorov-Smirnov test). The lower and upper solid lines of the boxplots correspond to the first and third quartiles of the data, the dash lines correspond to each individual data, and the black lines in the middle of the boxes represent the median. The solid lines above the boxplots represent the samples used for the Kolmogorov–Smirnov test. e Distribution of genes over expression ranging from less than 1 RPKM, 1-10 RPKM, 10-50 RPKM, 50-100 RPKM and larger than 100 RPKM in MAR targeted genes and all genes. Fisher’s exact test, **P < 0.01, ***P < 0.001. f Metagene plot showing the average distribution of MAR enrichment over protein-coding genes grouped by their expression levels (RPKM).