Fig. 1

Relationships between constitutive DNA methylation, expression, and chromatin accessibility in larval Strongylocentrotus purpuratus. A Median percent methylation averaged across CpGs in the promoter, introns, and exons per gene is plotted against transcript abundance measured as logCPM. Each point depicts a single gene. B A binary value representing whether or not a gene was found to have transcript variants is plotted across averaged median methylation of genes’ promoters, introns, and exons. Small black points depict single genes. Large blue points depict average DNA methylation among genes with or without transcript variants ± 95% CI. T/F values are spread across the y-axis to reduce overlap among points and better visualize their distribution across CpG methylation. C A loess trend of mean ATAC-seq read density (i.e., chromatin accessibility) ± 95% CI is plotted across distance to transcriptional start sites (TSS). D A 50-bp sliding window average of % CpG methylation ± 95% CI is plotted across distance to accessible chromatin regions for which all ATAC-seq replicates shared consensus for accessibility. n = 12 RNA-seq and RRBS replicate libraries; n = 3 ATAC-seq replicate libraries