Genome-wide analysis highlights causal epigenetic link to age at menarche

Age at menarche, a key milestone in female reproductive development, has declined globally and is associated with cancer and other health outcomes. We investigated epigenetic mechanisms underlying pubertal timing by analysing genome-wide DNA methylation in blood from 3,429 women (mean age 56 years) using the Illumina HumanMethylation450 BeadChip. In the discovery cohort, comprising 479 participants from the Australian Mammographic Density Twins and Sisters Study and 2,614 from the Melbourne Collaborative Cohort Study, we identified 63 differentially methylated regions. Of these, the TRIM61 region was replicated (P<0.05) in 336 women from the European Prospective Investigation into Cancer and Nutrition-Italy, showing consistent positive effects for each CpG and for the region overall. Mendelian randomisation suggested that TRIM61 methylation causally influences age at menarche and regulates the expression of nearby genes, including RP11-366M4.11. Functional annotation revealed the replicated region overlaps with active regulatory elements, suggesting that methylation at these sites may influence the expression of nearby genes through modulation of chromatin accessibility and transcriptional regulation. These findings identify a novel, causally implicated epigenetic mechanism at TRIM61, where methylation changes in active regulatory regions may alter chromatin accessibility and gene expression to influence pubertal timing. By integrating epigenome-wide association, Mendelian randomisation, and functional annotation, this work provides molecular evidence for novel regulatory pathways underlying age at menarche, offering new mechanistic insights into female reproductive development and its links to long-term health.