Figure 3

DNA methylation is enriched in the intergenome and on transposons. (A). RRBS Genomic Annotation on 120 hpf zebrafish livers of the CpGs common to the unified dataset of 3 biological replicates from 120 WT zebrafish larvae (2,173,502 CpGs). CpGs were categorized as methylated (>80%; 1,521,222 CpGs) and unmethylated (<20%; 427,492 of CpGs) and then were classified based on annotated genomic elements. The distribution of CpGs in the whole genome is plotted as a comparison. (B). Density plot showing the distribution of CpGs based on methylation level. (C). Annotation of CpGs contained in the Repetitive Elements (REs) or not-RE in zebrafish genome and RRBS dataset. (D). Box plot displaying the percent of methylation of CpGs contained in each Class of Transposable Elements (TEs) and not-TEs. (E). Violin plot displays the percent of CpG methylation in zebrafish livers contained inside (blue) or outside (grey) ATAC-Seq peaks. An equal number of CpGs (11,034 CpGs) contained outside of ATAC-seq peaks were randomly selected for comparison. **** indicates p-value < 0.0001 calculated by unpaired non-parametric Mann–Whitney test. (F). Box plot displaying the percent of CpGs either methylated (red, >80%) or not-methylated (grey, <20%) in WT livers: From left, CpGs contained inside (represented with +) or outside (represented with −) of ATAC-Seq peaks classified based on their location in annotated genomic element (promoters, exons, and introns). p-values were calculated by unpaired non-parametric multiple comparisons Kruskal-Wallis test. *** means p-value < 0.001.