Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta

ABSTRACT

5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in ‘open sea’ regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.

KEYWORDS:

• Hydroxymethylation
• gene expression
• eQTHM
• placenta

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Raw data were generated at Emory University. Derived data supporting the findings of this study are available through the Gene Expression Omnibus (GEO, accession number: GSE144129).

Ethical standards

All enrolled participants provided written informed consent and study protocols were approved by the institutional review boards (IRB) at WIH and Emory University.

Supplemental material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2024.2326869

Additional information

Funding

This work was supported by grants from the National Institutes of Health, National Institute of Environmental Health Sciences [P30ES 019776, U24 ES028507, R21 ES028226] and Eunice Kennedy Shriver National Institute of Child Health and Development [R01 HD108310].