Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects

Margarita Alfimova,Vera Golimbet,Nikolay Kondratyev,Arkadiy Golov

doi:10.1038/s41598-020-61671-2

Abstract

Interrogating DNA methylation within schizophrenia risk loci holds promise to identify mechanisms by which genes influence the disease. Based on the hypothesis that allele specific methylation (ASM) of a single CpG, or perhaps CpH, might mediate or mark the effects of genetic variants on disease risk and phenotypes, we explored haplotype specific methylation levels of individual cytosines within a genomic region harbouring the BAG5, APOPT1 and KLC1 genes in peripheral blood of schizophrenia patients and healthy controls. Three DNA fragments located in promoter, intronic and intergenic areas were studied by single-molecule real-time bisulfite sequencing enabling the analysis of long reads of DNA with base-pair resolution and the determination of haplotypes directly from sequencing data. Among 1,012 cytosines studied, we did not find any site where methylation correlated with the disease or cognitive deficits after correction for multiple testing. At the same time, we determined the methylation profile associated with the schizophrenia risk haplotype within the KLC1 fourth intron and confirmed ASM for cytosines located in the vicinity of rs67899457. These genetically associated DNA methylation variations may be related to the pathophysiological mechanism differentiating the risk and non-risk haplotypes and merit further investigation.

Highlights

Schizophrenia is a common, highly heritable disorder characterized by positive, negative, and cognitive symptoms
MQTL are often colocalized with expression QTL, which is in line with the hypothesis that allele-specific methylation (ASM) may be a cause or a result of allele specific transcription factor binding[27,28]
We evaluated the level of methylation of each cytosine, in both the CpG and non-CpG context, within three fragments of one of the top schizophrenia risk loci on chromosome 14 overlapping with an intelligence genome-wide association studies (GWAS) locus

Summary

Results

Average methylation values for each cytosine within the Fr_BAG5_APOPT1 fragment by group and haplotype and nominally significant p-values (p < 0.05) for every analysis conducted are given in Supplementary Table S5. In accord with the exploratory factor analysis described above, the network analysis of the sites with ASM revealed several groups of strongly connected consecutive CpGs and no clustering of CpHs (Fig. 5, the associated information can be found in Supplementary Tables S8a–d). This suggests that ASM at these CpH sites might be a mechanistic, non-specific consequence of CpG methylation in the CpG-SNP rich region.

Discussion

Methods