Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System Characterized by Whole Genome Bisulfite Sequencing (WGBS)

Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed bisulfite whole genome bisulfite methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, to compare tissue-related and injury-induced differences in DNA methylation among them. Whole Genome Bisulfite Sequencing (WGBS: 15XGenome coverage per sample) was performed on 21 samples (3 biological replicates; 7 tissues/conditions): operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at 11 days post optic nerve crush, plus surgically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at 7 days post spinal cord transection, with 5 pooled hindbrains for each sample; juvenile frog hindbrain at 7 days after spinal cord transection, plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.