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Fig. 1 | BMC Genomics

Fig. 1

From: Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System

Fig. 1

Chromosome-wide overview of injury-induced changes in DNA methylation for regenerative (tadpole) vs. non-regenerative (post-metamorphic frog) hindbrain after spinal cord injury (SCI) for two representative chromosomes (180 Mb of Chr 2L, top; 104 Mb of Chr 9_10S, bottom) as revealed by whole genome bisulfite sequencing (WGBS). Tracks for regenerative tadpole and non-regenerative frog hindbrain are grouped separately (Tad, top; Frog, bottom). For each chromosome, the vertical scales, which indicate the level of methylation (5mC) in each methylation context (CpG, dark green; CHG, olive green; CHH, navy blue), were group-autoscaled across tadpole and frog SCI and controls to facilitate comparisons between injury conditions (SCI vs. control) and developmental stage (tadpole vs. frog). Methylation differences between SCI and control (ΔCpG, ΔCHG, ΔCHH) indicate log2(SCI 5mC/control 5mC). The resulting increased (>0) and decreased methylation (<0) levels are shown in light green vs. blue, above and below the horizontal axes, respectively. Changes in RNA expression between SCI and control are also indicated (ΔRNA-Seq Tad and Frog; log2(SCI/control), with red and blue indicating increased and decreased expression, respectively [11]; note, RNA-Seq and WGBS were performed on RNA and DNA, respectively, isolated from the very same animals. H3K4me3 peaks at gastrulation (st. 10.5, [41]) and the locations of annotated genes (gene models: Mayball [21; 88; 89]; X. laevis v. 9.1 [122]) are also indicated. For all three DNA methylation contexts (CpG, CHG, CHH), methylation levels increased between tadpole and frog stages pervasively across the entire chromosome, and SCI induced opposite, pervasive methylation responses (ΔCpG, ΔCHG, ΔCHH) in tadpole vs. frog [increased (light green) vs. decreased (light blue) methylation, respectively]. As illustrated in these two representative examples, similar patterns were seen for all chromosomes, with no overall differences between L and S homeologous chromosomes

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