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

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• 5-Methylcytosine (5mC) is a key epigenetic mark in the human genome.
• Short-read sequencing for 5mC detection has limitations like PCR bias and restricted long-range analysis.
• Nanopore long-read sequencing offers a potential solution to these challenges.

Purpose of the Study:

• To profile the human methylome using nanopore long-read sequencing.
• To perform long-range co-methylation analysis and identify methylation haplotype blocks (MHBs).
• To investigate epigenetic changes associated with protein binding and noncoding genetic variants.

Main Methods:

• Adaptive sampling nanopore long-read sequencing targeting CpG islands and mQTL/GWAS regions.
• Linkage disequilibrium (LD) R² analysis to identify MHBs.
• Integration with ATAC-seq data to assess allele-specific accessibility.

Main Results:

• Cancer genomes show smaller MHBs and lower methylation LD R² compared to normal cells.
• Long-read sequencing effectively captures large MHBs, outperforming short-read methods.
• Identified allele-specific methylation and accessibility near GWAS risk variants.

Conclusions:

• Nanopore sequencing is feasible for comprehensive methylome profiling, preserving haplotype information.
• This approach provides novel insights into epigenetic modifications driven by noncoding variants.
• Enables detailed analysis of epigenetic regulation in cancer and other diseases.