41 / 2026-03-25 10:41:43

Single-base-resolution DNA methylome profiling reveals repeat-driven genomic constraint and regulatory innovation in domestic ruminants

DNA methylation,domestic ruminants,long-read sequencing,repetitive elements

Abstract

DNA methylation is an essential epigenetic mechanism in animals. However, limited sample sizes and reliance on short-read sequencing have hindered accurate detection of methylation differences in domestic ruminants. Here, leveraging HiFi long-read sequencing, we constructed a single-base-resolution blood DNA methylation atlas comprising 49 breeds from 717 pooled individuals across four domestic ruminants. On average, 27.46 million CpG sites, 60,989 hypomethylated regions, and 158,886 hypermethylated regions were identified per species. Global methylation divergence among ruminants was predominantly associated with repetitive regions. Notably, a 4.10% difference in non-centromeric methylation levels was observed between cattle and sheep, with repetitive regions accounting for ~75% of this divergence. Furthermore, species-specific hypomethylated regions were preferentially enriched for repeat-associated hypomethylation compared to conserved ones, suggesting repeat-driven regulatory divergence. We also identified 20 genes with repeat-associated methylation and expression divergence between taurine and indicine cattle. In particular, a repeat-derived structural variant modulates methylation of the Insulin Induced Gene 1 (INSIG1) enhancer, driving expression divergence and potentially affecting fat metabolism. This study provides a high-resolution methylation landscape for four domestic ruminants. It demonstrates that repeat-associated methylation enforces genomic constraint, whereas alterations in methylation patterns facilitate regulatory innovation. These findings offer mechanistic insights into the epigenetic architecture underlying ruminant diversification.