DNA methylation in peripheral tissues and left-handedness

Abstract

Handedness has low heritability and epigenetic mechanisms have been proposed as an etiological mechanism. To examine this hypothesis, we performed an epigenome-wide association study of left-handedness. In a meta-analysis of 3914 adults of whole-blood DNA methylation, we observed that CpG sites located in proximity of handedness-associated genetic variants were more strongly associated with left-handedness than other CpG sites (P = 0.04), but did not identify any differentially methylated positions. In longitudinal analyses of DNA methylation in peripheral blood and buccal cells from children (N = 1737), we observed moderately stable associations across age (correlation range [0.355-0.578]), but inconsistent across tissues (correlation range [- 0.384 to 0.318]). We conclude that DNA methylation in peripheral tissues captures little of the variance in handedness. Future investigations should consider other more targeted sources of tissue, such as the brain.

Figure 1

Flowchart of epigenome-wide association study of left-handedness. The flowchart summarizes the study design. The primary analyses included EWASs in NTR adults and ALSPAC adults, followed by meta-analysis to identify DNA methylation sites associated with left-handedness. The secondary analyses included: (1) left-handedness GWAS loci follow-up; (2) longitudinal analysis of DNA methylation at four ages in ALSPAC offspring; (3) analysis of buccal cell DNA methylation in NTR children; (4) analysis of DNA methylation differences between left and right-handed co-twins from NTR discordant MZ twin pairs and (5) polygenic and DNA methylation scores prediction. For left-handedness prediction, polygenic scores (PGS) were created based on left-handedness GWAS summary statistics not including NTR/ALSPAC. Methylation scores (MS) were created based on weights from EWASs in NTR adults, ALSPAC adults, NTR children and ALSPAC offspring at 7 years old to estimate the predictive performance. LH, left-handed; RH, right-handed. DMR, differentially methylated region. EWAS, epigenome-wide association study. GWAS, genome-wide association study. GoDMC, Genetics of DNA Methylation Consortium. mQTL, methylation quantitative trait locus. Blood, buccal cells indicate tissue of DNA methylation. 450 k, EPIC indicate the platform for DNA methylation measurement.

Figure 2

Differentially methylated regions associated with left-handedness in meta-analysis. The figure represents the differentially methylated regions at P-adjusted < 0.05 in meta-analysis of DMR statistics across groups of NTR adults and ALSPAC adults (N = 3712). The top panel of each plot depicts the EWAS P-values for CpGs in the differentially methylated regions (A) at chromosome 20; and (B) at chromosome 2. The x-axis indicates the position in base pair (bp) for the region, while y-axis indicates the strength of association from meta-analysis EWAS with left-handedness (adjusted model). The middle panel shows the genomic coordinates (genome build GRCh37/hg19) and the functional annotation of the region: the ENSEMBL Genes track shows the genes in the genomic region (orange); the CpG Island track shows the location of CpG islands (green); the Regulation ENSEMBL track shows regulatory regions (blue). CpGs from DMR associated with left-handedness are indicated with red lines above the correlation heatmap. More detailed information on the regions is provided in Table 4. The bottom panel shows the Spearman correlation between methylation levels of CpGs in the window. The figure was computed using the R package coMET. See additional information on CpGs from the regions in Supplementary Table 12.

Figure 3

Seven-step approach to DNA methylation signature discovery, incorporating twin design. The figure represents the methodology of DNA methylation signature discovery study of a phenotype in multiple steps. It integrates behavioral-genetic and SNP-based methods (step 1) to estimate heritability, epigenome-wide study methods (steps 3–4) for association analyses, follow-up of results using summary statistics from previous EWASs and GWASs (step 5), the discordant twin design (step 6), and methods integrating polygenic and DNA methylation data (step 7) in enrichment analysis. Specific methods for each step are presented on the left and outcomes on the right. GWAS, genome-wide association study. EWAS, epigenome-wide association study. SNP, single nucleotide polymorphisms. CpG, cytosine-phosphate-guanine. PGS, polygenic scores. MS, methylation scores. DMPs, differentially methylated positions. DMRs, differentially methylated regions.