A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta

Abstract

Background Human placental DNA methylation (DNAme) data is a valuable resource for studying sex differences during gestation, as DNAme profiles after delivery reflect the cumulative effects of gene expression patterns and exposures across gestation. Here, we present an analysis of sex differences in autosomal DNAme in the uncomplicated term placenta (n = 343) using the Illumina 450K array. Results At a false discovery rate < 0.05 and a mean sex difference in DNAme beta value of > 0.10, we identified 162 autosomal CpG sites that were differentially methylated by sex and replicated in an independent cohort of samples (n = 293). Several of these differentially methylated CpG sites were part of larger correlated regions of sex differential DNAme. Although global DNAme levels did not differ by sex, the majority of significantly differentially methylated CpGs were more highly methylated in male placentae, the opposite of what is seen in differential methylation analyses of somatic tissues. Patterns of autosomal DNAme at these 162 CpGs were significantly associated with maternal age (in males) and newborn birthweight standard deviation (in females). Conclusions Our results provide a comprehensive analysis of sex differences in autosomal DNAme in the term human placenta. We report a list of high-confidence autosomal sex-associated differentially methylated CpGs and identify several key features of these loci that suggest their relevance to sex differences observed in normative and complicated pregnancies.

Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions

“…Though these studies varied in their methodological approach and probe filtering strategies, this result supports the conclusion that the majority of differentially methylated sites identified herein are placenta-specific. Consistent with this notion, our results did overlap well with a previous study 43 of full term placenta DNAm differences by fetal sex, capturing 146 of the 166 CpG sites identified in this study.

Figure 2 Single site discovery in full term placenta samples.

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Maternal Metabolic State and Fetal Sex and Genotype Modulate Methylation of the Serotonin Receptor Type 2A Gene (HTR2A) in the Human Placenta

“…The extent of methylation at all four sites was higher in placentas of male than of female neonates. This observation is consistent with a recent study showing that most autosomal loci with sex-dependent DNA methylation in human term placenta are more highly methylated in male than in female placentas [ 65 ].…”

Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array

“…Consistent with this, we were able to replicate 75% of our saDMPs identified in our validation data set in our discovery data set. Moreover, we found that 73% of the saDMPs we identified in this study were also identified by Inkster and colleagues [ 27 ], whom also applied effect size cut offs, demonstrating the reproducibility and robustness of our catalogue of saDMPs.…”

“…We also additionally checked the overlap between our saDMPs identified in blood with those identified in other tissues (Table 2 ). Interestingly, we observe a 73% overlap with sex-associated sites identified in placenta by Inkster et al [ 27 ] and a 35% overlap with sex-associated sites identified in post-mortem prefrontal cortex [ 66 ]. The existence of this overlap between different tissues shows that a portion of these saDMPs identified are conserved across tissues, and that some are tissue specific.…”

“…This is not surprising as it has been previously reported that autosomal sex differences in DNA methylation result in nominal or no differences in gene expression [ 26 , 28 ], a trend also seen with age specific DNAme marks [ 51 ]. Moreover, while other studies claim that they identify DEGs on autosomes between males and females, corresponding to differences in DNA methylation, when adjusting for multiple testing, it appears that these no longer hold statistical significance [ 27 ]. It is also important to note that, the relationship between DNAme with gene expression is a complex one, although it is generally thought that DNA methylation leads to gene repression, lots of literature reports methylation leading to active expression [ 52 – 54 ] or that it is insufficient to repress transcription [ 55 ].…”