Fine mapping regulatory variants by characterizing native CpG methylation with nanopore long-read sequencing

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value compared to normal cells. Additionally, we demonstrated the superiority of long-read sequencing in capturing large MHBs compared with short-read sequencing. By profiling the methylation changes near the JASPAR motif and actual chromatin immunoprecipitation sequencing (ChIP-seq) peaks, we also studied the epigenetic changes related to protein binding. Based on adaptive sampling technology, we conducted nanopore sequencing targeting regions with methylation quantitative trait loci (mQTLs) and genome-wide association study (GWAS) risk variants in the 22Rv1 cell line. After analyses, we inspected the closest haplotype-specific methylated region near the variant and identified allele-specific methylated regions with allele-specific accessibility signals in the ATAC-seq data. This study demonstrates the feasibility of nanopore sequencing for methylome profiling while preserving haplotype information, offering an innovative approach to elucidate the epigenetic changes driven by noncoding variants in the human genome.

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