The heritability and patterns of DNA methylation in normal human colorectum

Abstract

DNA methylation (DNAm) has been linked to changes in chromatin structure, gene expression and disease. The DNAm level can be affected by genetic variation; although, how this differs by CpG dinucleotide density and genic location of the DNAm site is not well understood. Moreover, the effect of disease causing variants on the DNAm level in a tissue relevant to disease has yet to be fully elucidated. To this end, we investigated the phenotypic profiles, genetic effects and regional genomic heritability for 196080 DNAm sites in healthy colorectum tissue from 132 unrelated Colombian individuals. DNAm sites in regions of low-CpG density were more variable, on average more methylated and were more likely to be significantly heritable when compared with DNAm sites in regions of high-CpG density. DNAm sites located in intergenic regions had a higher mean DNAm level and were more likely to be heritable when compared with DNAm sites in the transcription start site (TSS) of a gene expressed in colon tissue. Within CpG-dense regions, the propensity of the DNAm level to be heritable was lower in the TSS of genes expressed in colon tissue than in the TSS of genes not expressed in colon tissue. In addition, regional genetic variation was associated with variation in local DNAm level no more frequently for DNAm sites within colorectal cancer risk regions than it was for DNAm sites outside such regions. Overall, DNAm sites located in different genomic contexts exhibited distinguishable profiles and may have a different biological function.

Figure 1.

Distribution of mean site-specific DNAm level with respect to CpG density. Methylation levels were measured on the M-value scale where a DNAm level of 0 can be interpreted as a 50% methylation level, a DNAm level of <0 and a DNAm level of >0 indicate < and >50% methylation, respectively. The majority of DNAm sites in islands exhibited a low-average methylation level, which was in contrast to the majority of DNAm sites in low-density CG regions (sea) being on average highly methylated.

Figure 2.

Mean site-specific DNAm level as a function of distance from the edge of the island. The 4000 BP region upstream (North) and downstream (South) of islands was divided into bins of 100 BP. The average of the mean site-specific DNAm levels for DNAm sites residing within each bin is shown as a circle enclosed by a line indicating ±2 standard error of the mean estimate. A shore is up to 2000 BP from an island and a shelf is between 2000 and 4000BP from an island.

Figure 3.

Distribution of mean site-specific DNAm level for eight contextual groups.

Figure 4.

Moments of the distributions of mean site-specific DNAm level for eight contextual groups.

Figure 5.

Distribution of the variance of each DNAm site used in analysis (n = 196080).

Figure 6.

Distribution of the estimated heritability for DNAm sites significantly associated with local genetic variation. Each bar represents a range of 0.05.

Figure 7.

The number of SNPs ±1 MB surrounding a DNAm site.

Figure 8.

Distribution of mean-site specific heritability for DNAm level in genes expressed in whole colorectal biopsies and colon epithelial cells. DNAm sites have a significant heritability if P < 0.05. Genes expressed in both the epithelial and WCB were removed from the WCB group for this analysis.

Figure 9.

The mean genetic variance and the proportion of heritable DNAm sites for the eight contextual groups. The x-axis value represents the proportion of heritable DNAm sites within each contextual group and the average genetic variance for each contextual group.

Figure 10.

Proportion of the regional heritability that can be explained by the top SNP association. The variance explained by a SNP (R²) divided by the regional heritability estimate for DNAm sites with a regional heritability estimate significant at P < 0.05. Only the most significant SNP within the local region was considered. In 4.2% of cases the SNP explained more variance in the DNAm level than did the region.