Trimester-specific associations of methyl-donor nutrients and prenatal dietary patterns with adolescent blood leukocyte circadian gene DNA methylation.

The prenatal period is critical for the development of the circadian system, with maternal diet potentially influencing its regulation through DNA methylation of circadian genes. This study examined the associations between prenatal dietary patterns and methyl-donor nutrient intake with DNA methylation of circadian genes in adolescents in the Early Life Exposure in Mexico to ENvironmental Toxicants cohort. Among 392 participants, trimester-specific dietary intake was assessed using food frequency questionnaire. Dietary patterns were derived from energy-adjusted food groups. Blood leukocyte DNA methylation was measured in adolescence using the Infinium MethylationEPIC BeadChip. Linear regression estimated associations at 707 cytosine-guanine sites across 18 circadian genes and in an epigenome-wide association study (EWAS) of 745,797 sites. False discovery rate of 5% was applied using the Benjamini-Hochberg method. First-trimester riboflavin intake was positively associated with DNA methylation at loci in RORA (probe ID cg08700690) and NR1D2 (cg21029468), while vitamin B12 intake was negatively associated with RORA (cg13576304). Second-trimester Transitioning Mexican Diet was positively associated with RORA (cg27391826). Third-trimester methionine intake was negatively associated with DNA methylation near the promoter region of RORA (cg10133825) and positively associated with a locus in PER1 (cg27004243), and the High Meat & Fat Diet was negatively associated with CLOCK (cg07327568). More associations were observed with gestational dietary patterns in males than females. EWAS identified multiple associations with methionine and vitamin B6 intake, including two circadian genes (BHLHE40 and RORA). Trimester-specific maternal intake of riboflavin, vitamin B12, and methionine were associated with DNA methylation at circadian gene loci assessed during adolescence.