Enjoy the silence: X-chromosome inactivation diversity in somatic cells

Abstract

The imbalance of sex chromosomes between females (XX) and males (XY) necessitates strict regulation of X-linked gene expression. X-Chromosome Inactivation (XCI) selects one X for transcriptional silencing in the early embryo, generating an epigenetically distinct and transcriptionally silent X that is maintained into adulthood. Some genes on the inactive X escape XCI, and human somatic cells have a greater number of escape genes compared to mice. Advances with single-cell technologies have revealed human-specific escape genes in fibroblasts and immune cells, some of which exhibit cell and tissue specificity. Here, we review recent discoveries of dynamic XCI in female immune cells, which have changed our understanding of XCI maintenance, and discuss how some X-linked genes might become overexpressed in female-biased autoimmunity.

Figure 1:. Xist RNA is dynamically localized to the Xi in developing lymphocytes and mature immune cell types.

(A) Schematic cartoon of Xist RNA localization changes in developing B lymphocytes in bone marrow (top) and T cell progenitors in the thymus (bottom). Xist RNA is absent from the Xi in pro-B and DN1 progenitors, and transiently re-appears at the Xi during differentiation. (B) Diversity of Xist RNA localization patterns in immune cell progenitors and seven different mature immune cell types. Xist RNA is not detectable by RNA fluorescence in situ hybridization (FISH) in naïve follicular (FO) B cells, naïve mature CD4+ and CD8+ T cells, and p-DCs. In stimulated B and T lymphocytes, Xist RNA transcripts are tightly clustered to the Xi. Dendritic cells (DCs), bone marrow derived macrophages (BMDMs), and NK T cells have distinct and dispersed patterns of Xist RNA localization. Plasmacytoid dendritic cells (p-DCs), resting and in vitro activated, always lack detectible Xist RNA signals. Red dots represent RNA FISH results for Xist RNA. Abbreviations: HSC (hematopoietic stem cell), CLP (common lymphoid progenitor), CMP (common myeloid progenitor), DN1-DN4 (double negative thymocytes stages 1–4), BMDM (bone marrow derived macrophage), m-DC (myeloid-Dendritic cell), NK T cell (Natural killer T cell), L-DC (lymphoid-Dendritic Cell), p-DC (plasmacytoid dendritic cell).

Figure 2:. Model for active or passive mechanisms that may regulate dynamic Xist RNA localization during lymphocyte activation.

Mature naïve lymphocytes lack Xist RNA on the Xi, and antigen stimulation triggers Xist RNA return to the Xi. We propose that this re-localization process could occur through either a passive (top) or active (bottom) mechanism. Our passive regulation model posits that unfolded/unstructured Xist RNA transcripts are dispersed across the nucleus, preventing cytological detection. Lymphocyte activation increases levels of Xist RNA interacting proteins, including YY1 and HnRNP-U, which could fold and tether Xist RNA transcripts to the Xi. Alternatively, re-localization could occur via an active process, where in naïve cells we propose that Xist RNA interacting proteins bind and sequester Xist RNA transcripts (perhaps in 1:1 stoichiometry), thereby preventing visualization by RNA FISH. Lymphocyte activation increases the concentrations of Xist RNA interacting proteins, including YY1 and HnRNP-U, which could bind to either one or multiple Xist transcripts. Xist RNA interacting factors then recruit Xist RNA to the Xi and tether Xist RNA transcripts across this chromosome. The active and passive mechanisms are not mutually exclusive. The absence of Xist RNA and heterochromatin marks at the Xi in naive cells may “relax” XCI maintenance and increase the number of genes escaping from XCI, such as Tlr7.