Simultaneous X-chromosome inactivation and tissue-/cell-type-specific DNA methylation in the transcriptional regulatory region of the X-linked recessive disease gene OTC

Variability in disease onset and severity among heterozygous females with X-linked recessive disorders, such as ornithine transcarbamylase (OTC) deficiency, may result from differences in the expression level of the normal allele caused by skewed X-chromosome inactivation (XCI). However, previous studies on the mechanisms of XCI lack relevance to humans. By applying the concept of hypomethylated allele frequency, gene expression can be estimated through DNA methylation analysis of transcriptional regulatory regions, including tissue-/cell-type-specific differentially methylated regions (T-DMRs) and XCI-affected regions. In this study, we identified a porcine OTC transcriptional regulatory region that functions both as a T-DMR and XCI-affected differentially methylated region. Furthermore, by distinguishing alleles using a single nucleotide polymorphism, we detected evidence of skewed XCI in female pigs. Accordingly, by demonstrating that hypomethylated allele frequency reflects the active X allele, this study provides possible molecular evidence of skewed X inactivation through DNA methylation within the OTC T-DMR.