Journal Article

Interplay of the Genetic Variants and Allele Specific Methylation in the Context of a Single Human Genome Study

Zayakina, Olga V., Tarasova, Darya A., Keskinov, Anton A., Yudin, Sergey M., Yudin, Vladimir S., Deinichenko, Kseniia A., Grebnev, Pavel Alekseevich, Voronina, Maria D., Svetlichnyy, Dmitry V., Tsimmer, Olga Y., Shingalieva, Olga Sergeevna, Skvortsova, Veronika I., Snigir, Ekaterina A., Mitrofanov, Sergey I.

2025

Overview

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans.

• Publisher: MDPI AG
• Subject: Alleles / Blood proteins / Chromatin / Comparative analysis / CpG Islands - genetics / Disease / DNA / DNA methylation / DNA Methylation - genetics / DNA sequencing / Epigenesis, Genetic / Epigenetic inheritance / Epigenetics / Gene expression / Genes / Genetic aspects / Genetic research / Genetic Variation / Genome, Human / Genomes / Genomics / Haplotypes / Health risk assessment / Humans / Information management / Mediation / Methylation / Nucleotide sequencing / Polymorphism, Single Nucleotide / RNA / RNA sequencing / Sequence Analysis, DNA / Whole Genome Sequencing