Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable

Abstract

X-chromosome inactivation (XCI) silences one X in female cells to balance sex-differences in X-dosage. A subset of X-linked genes escape XCI, but the extent to which this phenomenon occurs and how it varies across tissues and in a population is as yet unclear. To characterize incidence and variability of escape across individuals and tissues, we conducted a transcriptomic study of escape in adipose, skin, lymphoblastoid cell lines and immune cells in 248 healthy individuals exhibiting skewed XCI. We quantify XCI escape from a linear model of genes’ allelic fold-change and XIST-based degree of XCI skewing. We identify 62 genes, including 19 lncRNAs, with previously unknown patterns of escape. We find a range of tissue-specificity, with 11% of genes escaping XCI constitutively across tissues and 23% demonstrating tissue-restricted escape, including cell type-specific escape across immune cells of the same individual. We also detect substantial inter-individual variability in escape. Monozygotic twins share more similar escape than dizygotic twins, indicating that genetic factors may underlie inter-individual differences in escape. However, discordant escape also occurs within monozygotic co-twins, suggesting environmental factors also influence escape. Altogether, these data indicate that XCI escape is an under-appreciated source of transcriptional differences, and an intricate phenotype impacting variable trait expressivity in females.

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

“…We confirmed substantial variability across different NPC clones in the numbers of escapees per clone, ranging from 48 to 124 genes escaping XCI out of 379 X-linked genes for which we have allelic information, as previously shown [Extended Data Fig. 1d] 56, 57 and also consistent with human inter-individual data 4, 7, 20–22, 58 . We assessed whether higher levels of Xist RNA correlate with lower expression levels of escapees chromosome-wide and found a significant negative correlation (p=0.012, correlation test), suggesting that Xist may indeed play a role in tuning the dosage of X-linked escapees on the Xi [Fig.…”

“…How a subset of "escapee" genes avoid or override this silencing, to be biallelically expressed from both active (Xa) and inactive (Xi) X chromosomes is not known 18,19 . A small percent of X-linked escapees (~3-7% in mice and ~4-11% in humans [19][20][21][22] ) can evade silencing from the very onset of XCI. Such constitutive escape is found in most cell types and individuals and is conserved across different species 12,19 .…”

First report on female monozygotic twins discordant for congenital nephrogenic diabetes insipidus

“…Other mechanisms, such as environmental factors and DNA methylation, may also be involved. Furthermore, discordant XCI escape has been found in monozygotic co‐twins, which may impact variable trait expressivity in females (Zito et al, 2023). It is now believed that the difference between monozygotic twins is more profound than we know.…”

“…XCI patterns may vary across different tissues, which is influenced by genetic and environmental factors (Zito et al, 2023). However, this hypothesis has not been directly confirmed in female subjects with NDI.…”

“…Although most female cases showed skewed XCI patterns in peripheral blood leukocytes, random XCI patterns in peripheral blood leukocytes have been found in two female subjects (Table 1; Namatame‐Ohta et al, 2018; Satoh et al, 2008). The possible mechanism may be that XCI patterns may vary across different tissues, which is influenced by genetic and environmental factors (Zito et al, 2023). However, this hypothesis has not been directly confirmed in female subjects with NDI.…”