Associations between placental hydroxymethylation and birthweight

Area of Science:

• Epigenetics
• Developmental Biology
• Genomics

Background:

• 5-hydroxymethylcytosine (5hmC) is an oxidized derivative of 5-methylcytosine (5mC), primarily considered a DNA demethylation intermediate.
• Emerging evidence suggests 5hmC may possess independent functional roles beyond demethylation.
• Placental epigenetics, including DNA methylation and hydroxymethylation, is crucial for fetal development and birthweight outcomes.

Purpose of the Study:

• To conduct an epigenome-wide association study (EWAS) investigating the relationship between placental 5-hydroxymethylcytosine (5hmC) and newborn birthweight.
• To evaluate the impact of 5hmC signal on traditional epigenome-wide studies relying solely on bisulfite (BS) modification (measuring both 5mC and 5hmC).
• To determine if 5hmC plays a significant, independent role in regulating birthweight.

Main Methods:

• Parallel bisulfite and oxidative bisulfite modification of DNA extracted from placenta samples.
• Array-based assessment for quantifying 5hmC and 5mC levels across the epigenome.
• Epigenome-wide association study (EWAS) analysis correlating placental 5hmC/5mC levels with newborn birthweight data from the Rhode Island Child Health Study (RICHS).
• Comparative analysis of EWAS results using combined 5hmC+5mC data versus 5mC-only data.

Main Results:

• A significant association was identified between 5hmC at a specific CpG site within the CUBN gene and newborn birthweight (False Discovery Rate < 0.05).
• Expression of the CUBN gene was also found to be associated with birthweight, suggesting a functional link.
• A strong positive correlation (r = 0.77, p < 0.0001) was observed between effect estimates from EWAS using combined 5hmC+5mC and 5mC-only assessments.
• No widespread associations between placental 5hmC and birthweight were detected, indicating 5hmC may not be a major driver of birthweight variation.

Conclusions:

• Traditional epigenome-wide studies using bisulfite modification alone provide accurate assessments of CpG-specific DNA methylation for EWAS related to birthweight.
• While a specific 5hmC site in CUBN is linked to birthweight, the overall contribution of placental 5hmC to birthweight variation appears limited.
• The findings suggest that standard 5mC assessment is largely sufficient for detecting methylation-associated birthweight effects, but the functional role of 5hmC warrants further investigation.