Mammalian brains feature exceptionally high levels of non-CpG DNA methylation alongside the canonical form of CpG methylation. Non-CpG methylation plays a critical regulatory role in cognitive function, which is mediated by the binding of MeCP2, the transcriptional regulator that when mutated causes Rett syndrome. However, it is unclear whether the non-CpG neural methylation system is restricted to mammalian species with complex cognitive abilities or has deeper evolutionary origins. To test this, we investigated brain DNA methylation across 12 distantly related animal lineages, revealing that non-CpG methylation is restricted to vertebrates. We discovered that in vertebrates, non-CpG methylation is enriched within a highly conserved set of developmental genes transcriptionally repressed in adult brains, indicating that it demarcates a deeply conserved regulatory program. We also found that the writer of non-CpG methylation, DNMT3A, and the reader, MeCP2, originated at the onset of vertebrates as a result of the ancestral vertebrate whole-genome duplication. Together, we demonstrate how this novel layer of epigenetic information assembled at the root of vertebrates and gained new regulatory roles independent of the ancestral form of the canonical CpG methylation. This suggests that the emergence of non-CpG methylation may have fostered the evolution of sophisticated cognitive abilities found in the vertebrate lineage.

哺乳动物的大脑具有异常高水平的非 CpG DNA 甲基化以及典型的 CpG 甲基化形式。非 CpG 甲基化在认知功能中起着关键的调节作用，这是由 MeCP2 的结合介导的，MeCP2 是转录调节因子，当突变时会导致 Rett 综合征。然而，尚不清楚非 CpG 神经甲基化系统是否仅限于具有复杂认知能力的哺乳动物物种或具有更深层次的进化起源。为了测试这一点，我们调查了 12 个远缘动物谱系的大脑 DNA 甲基化，揭示非 CpG 甲基化仅限于脊椎动物。我们发现在脊椎动物中，非 CpG 甲基化在一组高度保守的发育基因中得到丰富，这些基因在成年大脑中被转录抑制，表明它划定了一个深度保守的监管程序。我们还发现非 CpG 甲基化的写入者 DNMT3A 和读取者 MeCP2 起源于脊椎动物的发病，这是脊椎动物祖先全基因组复制的结果。我们一起展示了这种新的表观遗传信息层如何在脊椎动物的根部组装，并获得了独立于经典 CpG 甲基化的祖先形式的新调节作用。这表明非 CpG 甲基化的出现可能促进了脊椎动物谱系中复杂认知能力的进化。我们展示了这种新的表观遗传信息层如何在脊椎动物的根部组装，并获得了独立于经典 CpG 甲基化的祖先形式的新调节作用。这表明非 CpG 甲基化的出现可能促进了脊椎动物谱系中复杂认知能力的进化。我们展示了这种新的表观遗传信息层如何在脊椎动物的根部组装，并获得了独立于经典 CpG 甲基化的祖先形式的新调节作用。这表明非 CpG 甲基化的出现可能促进了脊椎动物谱系中复杂认知能力的进化。