Methylation Mesa define functional regulatory elements for targeted gene activation [patients]

We hypothesized that causal regulatory elements are defined by biophysical hypersensitivity. Profiling 24 whole-genome bisulfite sequencing samples across diverse human and murine models, we identified Methylation Mesa, narrow (~45-300 bp), structurally conserved epigenetic regulatory elements.

Mesa show enrichment in 5’UTRs and correlates transcriptional activation significantly better than canonical promoters. To prove causality, we developed CRISPR-DiR, an RNA-based targeted demethylation technology offering greater spatial precision, higher potency, and reduced toxicity compared to CRISPR-TET1. Focal demethylation of a Mesa, but not the proximal promoter, drove exponential CDKN2A (p16) reactivation and robust in vivo tumor suppression.