Fig. 4

Degree of CpG methylation surrounding the transcriptional start site (TSS; ±2.0 kb) correlated with RNA expression for regenerative (tadpole) and non-regenerative (frog) hindbrain before and after SCI. Top, average level of CpG-methylation for different levels of gene expression (Q1 to Q4, representing the 25% most highly to least expressed genes, respectively from a total of 45,099 gene models in X. laevis v.9.1 [122]). (+ or -) Δ, indicates the injury-induced changes for genes in Q1. x-axis units, distance from the predicted transcription start site (TSS) in kilobases (kb); y-axis units (Methylation Density), number of 5mCs in a 50 bp bin x 1 million/total number of Cs. Bottom, heatmaps of CpG methylation for each quartile, clustered from highest to lowest. The degree of CpG-methylation exhibited the expected negative correlation with RNA expression, but for the top two quartiles, it increased in regenerative hindbrain and decreased in non-regenerative hindbrain after SCI. The degree of CpG methylation is indicated by the intensity of the color, as indicated to the right of each heatmap (Methylation Density)