Hi-C-derived insulation strength predicts evolutionary conservation of topologically associated domains

We generated bulk Hi-C contact maps from the ventral hippocampus of eight inbred mouse strains, including five classical laboratory strains and three wild-derived strains, comprising 14.55 billion valid contacts. We show that discrete TAD and loop calling yields poor inter-replicate concordance, whereas separation scores, a continuous measure of boundary insulation strength, substantially improve reproducibility.

Using this approach, we identified 2,857 highly insulated genomic regions whose insulation was conserved across all strains. These regions were enriched for multiple CTCF binding sites, accessible chromatin, and proximity to super-enhancers and housekeeping genes, and showed greater DNA sequence conservation across placental mammals and more stable DNA methylation than expected by chance. Genomic structural rearrangements were the primary driver of chromatin conformation differences between strains, were largely a readout of local sequence variation rather than a structure-driven effect.