Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus

Abstract

Organisms exposed to endocrine disruptors in early life can show altered phenotype later in adulthood. Although the mechanisms underlying these long-term effects remain poorly understood, an increasing body of evidence points toward the potential role of epigenetic processes. In the present study, we exposed hatchlings of an isogenic lineage of the self-fertilizing fish mangrove rivulus for 28 days to 4 and 120 ng/L of 17-α-ethinylestradiol. After a recovery period of 140 days, reduced representation bisulfite sequencing (RRBS) was performed on the liver in order to assess the hepatic genome-wide methylation landscape. Across all treatment comparisons, a total of 146 differentially methylated fragments (DMFs) were reported, mostly for the group exposed to 4 ng/L, suggesting a non-monotonic effect of EE2 exposure. Gene ontology analysis revealed networks involved in lipid metabolism, cellular processes, connective tissue function, molecular transport and inflammation. The highest effect was reported for nipped-B-like protein B (NIPBL) promoter region after exposure to 4 ng/L EE2 (+ 21.9%), suggesting that NIPBL could be an important regulator for long-term effects of EE2. Our results also suggest a significant role of DNA methylation in intergenic regions and potentially in transposable elements. These results support the ability of early exposure to endocrine disruptors of inducing epigenetic alterations during adulthood, providing plausible mechanistic explanations for long-term phenotypic alteration. Additionally, this work demonstrates the usefulness of isogenic lineages of the self-fertilizing mangrove rivulus to better understand the biological significance of long-term alterations of DNA methylation by diminishing the confounding factor of genetic variability.

Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements

“…We found most of the differential methylation in intergenic regions and on introns (Figure 2C,D,F,G). Although differential methylation of noncoding regions has been reported, 16–24 little is known about its biological functions. Initially, we used HOMER to determine motif enrichment in hypo‐ and hyper‐DMSs, and found motifs supporting our model and phenotype.…”

“…[13][14][15] To date, most studies have focused on probing the alterations in DNA methylation near genes and promoters, which are easier to mechanistically link to changes in gene expression. Nonetheless, there is a growing body of literature from different animal models, tissues, and cell types reporting on prevailing differential methylation in intergenic regions, introns, and other noncoding DNA regions, [16][17][18][19][20][21][22][23][24] following the contextual and environmental stimulus. These areas in the genome may harbor cis-and trans-regulatory elements of transcription, also known as enhancers.…”