Abstract
<jats:p>Profiling the regulatory DNA methylation landscape remains technically challenging. Reduced-representation bisulfite sequencing (RRBS) misses distal enhancers and non-canonical regulatory elements, while whole-genome bisulfite sequencing (WGBS) distributes reads genome-wide, limiting consistent recovery of informative CpGs across sample collections. Here we present eRREMS (enhanced Reduced Representation Enzymatic Methylation Sequencing), addressing both limitations by combining MspI and HaeIII digestion with enzymatic cytosine conversion. eRREMS approximately doubles regulatory CpG recovery relative to standard RRBS, outperforming TaqαI-based extended protocols, with gains concentrated in dynamically regulated enhancers, alternative promoters, and splicing-associated regions. HaeIII-specific CpGs capture additional complex trait heritability beyond standard RRBS. At modest, comparable sequencing depths, eRREMS achieves greater cohort-level completeness for regulatory and dynamically variable CpGs than WGBS and requires substantially fewer reads. CpG capture is stable across enzymatic conversion kits and library preparation conditions, supporting broad adoption. eRREMS provides a cost-efficient and reproducible strategy for scalable methylome profiling of regulatory CpGs across cohorts.</jats:p>