Background Sex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and females in some tissues, including differences in DNA methylation patterns. Here, we report for the first time an analysis of autosomal sex differences in DNAme using the Illumina EPIC array in human whole blood by performing a discovery (n = 1171) and validation (n = 2471) analysis. Results We identified and validated 396 sex-associated differentially methylated CpG sites (saDMPs) with the majority found to be female-biased CpGs (74%). These saDMP’s are enriched in CpG islands and CpG shores and located preferentially at 5’UTRs, 3’UTRs and enhancers. Additionally, we identified 266 significant sex-associated differentially methylated regions overlapping genes, which have previously been shown to exhibit epigenetic sex differences, and novel genes. Transcription factor binding site enrichment revealed enrichment of transcription factors related to critical developmental processes and sex determination such as SRY and ESR1. Conclusion Our study reports a reliable catalogue of sex-associated CpG sites and elucidates several characteristics of these sites using large-scale discovery and validation data sets. This resource will benefit future studies aiming to investigate sex specific epigenetic signatures and further our understanding of the role of DNA methylation in sex differences in human whole blood.

Background Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable. Results Here we presented a novel method to predict sex using only DNA methylation beta values, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only signal intensities) uploaded to GEO. We identified 4345 significantly (p<0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first principal components of the DNA methylation data of sex-associated probes mapped on sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case. Conclusions This proposed sex classifier not only can be used for sex predictions but also applied to identify samples with sex chromosome aneuploidy, and it is freely and easily accessible by calling the ‘estimateSex’ function from the newest wateRmelon Bioconductor package (https://github.com/schalkwyk/wateRmelon).

Mammalian genomes harbor a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition. Although most TEs are epigenetically repressed, transcriptional silencing is partially released to permit developmental or tissue-specific expression of TEs. Some TEs have also evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded transcription factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Previously, the noncoding long terminal repeat (LTR) part of the endogenous retrovirus (ERV) families has been shown to function as enhancers. We show that new LTR families and the promoter region of LINE1 (L1) are enriched with H4K16ac and H3K122ac and the chromatin features associated with active enhancers. Depletion of MSL complex and H4K16ac levels leads to a significant reduction in the expression of L1 and ERV/LTRs. We demonstrate that H4K16ac regulates TE transcription by maintaining a permissive chromatin structure. Furthermore, CRISPR-based perturbation of candidate TEs led to the downregulation of genes in cis. We conclude that H4K16ac and H3K122ac regulate a significant portion of the mammalian genome by opening local chromatin structure and transcriptional activity at TEs.