Flanking DNA sequences determine DNA methylation maintenance in proliferation, cancer and aging

DNA methylation is a stable epigenetic modification essential for promoter silencing, retrotransposon silencing, genomic imprinting, and X-chromosome inactivation. Symmetrical DNA methylation at CpG dinucleotides is maintained after every round of cell division by the DNMT1-UHRF1 maintenance methyltransferase complex. Here we define a conserved rank order of DNA hexanucleotide sequences surrounding CpG sites that determines baseline DNA methylation levels in cells and the probability that DNA methylation is retained across cell divisions. This rank order is conserved in vertebrates and does not depend on TET enzymatic activity. CpG sites in hexanucleotide sequences less favored by DNMT1 are more susceptible to replication-dependent loss of DNA methylation over time; consequently, the methylation status of these motifs serves as a marker of cumulative cell divisions, biological age and cancer progression. Thus, the intrinsic vulnerability stemming from the sequence preference of the DNMT1-UHRF1 complex compromises the long-term stability of DNA methylation, especially at heterochromatic sites in proliferating cells, and contributes to the epigenetic dysregulation observed in cancer and aging.