Consistency and Variability of DNA Methylation in Women During Puberty, Young Adulthood, and Pregnancy

Abstract

Prior DNA methylation (DNA-m) analyses have identified cytosine-phosphate-guanine (CpG) sites, which show either a significant change or consistency during lifetime. However, the proportion of CpGs that are neither significantly different nor consistent over time (indifferent CpGs) is unknown. We investigated the methylation dynamics, both longitudinal changes and consistency, in women from preadolescence to late pregnancy using DNA-m of peripheral blood cells. Consistency of cell type-adjusted DNA-m between paired individuals was assessed by regressing CpGs of subsequent age on the prior, stability by intraclass correlation coefficients (>0.5), and changes by linear mixed models. In the first 2 transitions (10-18 years and 18 years to early pregnancy), 19.5% and 20.9% CpGs were consistent, but only 0.35% in the third transition (from early to late pregnancy). Significant changes in methylation were found in 0.7%, 5.6%, and 0% CpGs, respectively. Functional enrichment analyses of genes with significant changes in DNA-m in early pregnancy (5.6%) showed that the maternal DNA-m seems to reflect signaling pathways between the uterus and the trophoblast. The transition from early to late pregnancy showed low consistency/stability and no changes, suggesting the presence of a large proportion of indifferent CpGs in late pregnancy.

Keywords: CpGs; DNA methylation; Puberty; change; consistency; pregnancy; stability.

Figure 1.

Manhattan plot for consistency of DNA methylation between different time periods in women (after cell type adjustment) between (A) age 10 and 18 years, (B) age 18 years and early pregnancy, and (C) early (weeks 20–21) and late pregnancy (>week 22). The black dashed line is a reference for FDR = 0.05.

Figure 2.

Volcano plots showing the regression coefficient of the paired DNA methylation measured at the latter time period on the level of the earlier measurement. The CpGs with statistically significant (FDR < 0.05) intra-individual regression coefficients are colored in red. Those with positive coefficients are plotted to the right and those with negative coefficients to the left. (A) Age 10 to age 18 years without adjustment for cell composition, (B) age 18 years to early pregnancy without adjustment for cell composition, (C) early (weeks 20-21) to late pregnancy (>week 22) without adjustment for cell composition, (D) age 10 to age 18 years with adjustment for cell composition, (E) age 18 years to early pregnancy with adjustment for cell composition, and (F) early (weeks 20-21) to late pregnancy (>week 22) with adjustment for cell composition. CpG indicates cytosine-phosphate-guanine; FDR, false discovery rate.

Figure 3.

Analysis of the stability of 218 222 CpGs using ICCs with and without prior adjustment for cell composition. (A) Age 10 to age 18 years without adjustment for cell composition—32 916 CpGs are stable with a threshold of ICC > 0.5. (B) Age 18 years to early pregnancy without adjustment for cell composition—29 832 CpGs are stable with a threshold of ICC > 0.5. (C) Early (weeks 20-21) to late pregnancy (>week 22) without adjustment for cell composition—6626 CpGs are stable with a threshold of ICC > 0.5. (D) Age 10 to age 18 years with adjustment for cell composition—35 134 CpGs are stable with a threshold of ICC > 0.5. (E) Age 18 to early pregnancy with adjustment for cell composition—31 748 CpGs are stable with a threshold of ICC > 0.5. (F) Early (weeks 20-21) to late pregnancy (>week 22) with adjustment for cell composition—290 CpGs are stable with a threshold of ICC > 0.5. CpG indicates cytosine-phosphate-guanine; ICC, intraclass correlation coefficient.