The eXceptional nature of the X chromosome

Abstract

The X chromosome is unique in the genome. In this review we discuss recent advances in our understanding of the genetics and epigenetics of the X chromosome. The X chromosome shares limited conservation with its ancestral homologue the Y chromosome and the resulting difference in X-chromosome dosage between males and females is largely compensated for by X-chromosome inactivation. The process of inactivation is initiated by the long non-coding RNA X-inactive specific transcript (XIST) and achieved through interaction with multiple synergistic silencing pathways. Identification of Xist-interacting proteins has given insight into these processes yet the cascade of events from initiation to maintenance have still to be resolved. In particular, the initiation of inactivation in humans has been challenging to study as: it occurs very early in development; most human embryonic stem cell lines already have an inactive X; and the process seems to differ from mouse. Another difference between human and mouse X inactivation is the larger number of human genes that escape silencing. In humans over 20% of X-linked genes continue to be expressed from the otherwise inactive X chromosome. We are only beginning to understand how such escape occurs but there is growing recognition that escapees contribute to sexually dimorphic traits. The unique biology and epigenetics of the X chromosome have often led to its exclusion from disease studies, yet the X constitutes 5% of the genome and is an important contributor to disease, often in a sex-specific manner.

Figure 1.

Major factors involved in the inactivation of an X. Xist RNA coats the X and is critical for its localization to either (or both) the nucleolus and nuclear membrane. Localization to the nucleolar membrane requires the lncRNA Firre. Xist acts as a molecular scaffold recruiting various repressive complexes such as PRC1/2 while also acting as a tether between various chromatin and matrix binding factors. Some of these factors, such as PRC2 and HNRNPU are known to be recruited to the Xi in both humans and mice, however most evidence of the interactions and pathways regulating these factors comes from work done in mouse models. H3/H4/H2A/H2B refer to histone subunits, me and ac refer to the methylation and acetylation of histone tails at specified lysines (K).

Figure 2.

Escape genes and putative elements involved. (A) Proportion of genes subject to, or escaping from, XCI. Both the escape and the subject category have a subcategory of ‘mostly’ subject/escape which include those genes for which multiple studies tend to agree, but there is an exception. The variable category includes both genes described within studies as variable (n=47), as well as those genes which consistently differ between studies (n=44). (B) Proposed elements involved in a gene’s ability to escape from XCI as applied to the RPS4X escape region in humans. RPS4X and neighbouring gene CITED1 (a variable gene whose expression status had been described as subject or escape) retain the ability to escape from XCI (CITED1 is brain-specific) when present on a BAC integrated into the mouse Hprt locus on the Xi. Evidence and candidates for waystations, boundary and escape elements are described in boxes.

Figure 3.

Impact of an inactive X on disease. For recessive alleles of genes subject to XCI, males will be affected at the population frequency ‘p’. Females will be homozygous at a much lower frequency (p², so if a trait is seen in 1 in a 1000 males, then it will be seen in 1 in a million females). However, the large heterozygous female population will be mosaic for the trait, with skewing influencing the extent of which each allele is expressed (shaded horizontal arrow). Carriers will only express the trait if a threshold of required product is not met, and an example of a disease threshold is shown as a dotted orange line. For dominant disorders the same frequencies apply; however, generally hemizygous or homozygous individuals do not survive and the disease manifests in carrier females. As escape genes are not fully expressed from the Xi, they will show similar impact of skewing on mosaicism, with a shift towards higher overall expression levels. Again, disease presentation will depend on the threshold of gene product required. Shown below is a comparison of expression levels between males and females for escape genes that retain or lack a Y homologue.