Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas

Abstract

Background: The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. Contrary to popular belief, the placenta forms mainly from fetal tissue; therefore, it has the same biological sex as the fetus it supports. However, while placental function is linked to increased risks of pregnancy complications and neurodevelopmental diseases in male offspring in particular, the sex-specific epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown. Methods: We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex-specific differences in transcription and DNA methylation. Results: Our sex-specific analysis revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Sex-specific differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several sex-specific DEGs were correlated with sex-specific DMRs. A subset of the sex-specific DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas, while others were acquired later in placental development. Conclusion: Our study provides comprehensive lists of sex-specific DEGs and DMRs that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.

Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure

“…Importantly, these ethanol-exposed DMRs and sex-biased regions exhibited distinct CpG distributions based on sex. Notably, we observed a higher proportion of female- specific DMRs located in sex-biased regions in CpG islands and shores than male-specific DMRs located in sex-biased regions (39). These differentially methylated regions between male and female embryos could help explain the sex-specific changes observed in both DNA methylation and gene expression.…”

“…S5A). These included methylation changes that were consistent (39) and opposing (50) between the sexes (Fig. S5A, S5B).…”

“…To evaluate the impact of early preimplantation alcohol exposure on genes crucial for placental development, we analyzed our DNA methylation and gene expression datasets using previously published curated gene lists (39).…”

“…In a recent study, we discovered genome regions with sex-biased DNA methylation profiles in control placentas at E18.5 (39). When we compared the DMRs observed following preimplantation alcohol exposure with these sex-biased regions, we found that 115 male DMRs and 188 female DMRs were also sex-biased at late gestation.…”