Fig. 3

Differential intron methylation affected expression conditional upon TSS accessibility and transcript abundance. A Differential gene expression in response to maternal upwelling is plotted against mean intron differential methylation. Rows and columns group data based on transcript abundance and transcriptional start site (TSS) accessibility quartiles. First and last rows/columns denote highest and lowest quartiles while the middle row/column denote second and third quartiles. B Log-scale inclusion Bayes factors depicting the probability of observed data under models with a parameter relative to those without it, including the interaction effect visualized in A (“methylation:chromatin:expression”). Positive Bayes factor values represent parameters that improved predictive strength across models and were jointly included in the selected model of differential expression responding to maternal conditioning. For parameters listed on the y-axis, “methylation” = intron differential methylation, “chromatin” = TSS accessibility, and “expression” = baseline gene expression (logCPM). n = 12 RNA-seq and RRBS replicate libraries; n = 3 ATAC-seq replicate libraries