An evolutionarily conserved DNA-encoded logic shapes CpG island formation. An evolutionarily conserved DNA-encoded logic shapes CpG island formation

DNA methylation is an epigenetic modification of the vertebrate genome that contributes to transcriptional repression, imprinting, and X-chromosome inactivation. While the majority of the genome is blanketed in DNA methylation, regions known as CpG islands (CGIs) remain remarkably refractory to this modification. CpG islands are associated with roughly two thirds of gene promoters, are evolutionarily conserved, and play central roles in gene regulation, yet how they are protected from DNA methylation remains enigmatic. Based on the conserved nature of CpG islands, we have exploited genomic approaches and a transchromosomic model system to ask if DNA sequence is sufficient to specify the hypomethylated state at CpG islands when a human chromosome is newly introduced into mouse. Interestingly, this approach revealed that promoter-associated CGIs remain immensely refractory to DNA methylation regardless of the host species, in fitting with their conservation across vertebrate species and revealing that DNA sequence is a central driver in this outcome. In contrast, the methylation state of distal elements is highly variable between species and is host nucleus dependent. These alterations in methylation state at distal elements are defined by DNA nucleotide frequency and occupancy of DNA binding transcription factors, uncovering a widespread role for these features in defining the how this aspect of the epigenome forms away from gene promoters. These central principles are further supported by transplantation of mouse DNA sequences into the evolutionarily distant zebrafish genome, revealing the existence of a highly conserved and DNA encoded logic that shapes the vertebrate epigenome. Overall design: Bio-CAP was used to identify hypomethylated regions of DNA in the transchromosomic mouse model Tc1, which contains an almost entire copy of human chromosome 21, and wildtype Tc0 mice in liver and testis tissues, and in zebrafish embryos in which mouse BAC DNA has been introduced into the genome.