FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos

DNA methylation plays a crucial role in development and disease. Bisulfite-free methods such as enzymatic methyl sequencing (EM-seq) offer gentle approaches for whole-genome analysis, but they typically depend on PCR-based library amplification, which distorts coverage and methylation quantification. Here, we introduce FINE (Fast Isothermal amplification via Nicking Enzyme), a robust isothermal amplification strategy that leverages a nicking enzyme-assisted strand displacement reaction and can amplify methylation libraries from sub-nanogram inputs in 20 min. FINE-EM-seq increases library efficiency and coverage uniformity compared to PCR-based approaches, minimizing amplification bias and improving methylation calling accuracy. Applied to zebrafish embryos at four early developmental stages, FINE-EM-seq characterized stage-associated methylation dynamics through blastulation and early gastrulation. Furthermore, our analysis revealed blastulation-associated differentially methylated regions (DMRs) overlapping with AT-rich regions that were previously under-covered. These results illustrate that FINE-EM-seq is a rapid, robust solution for low-input whole-genome methylation sequencing with broad utility in developmental biology and clinical epigenomics.