Spontaneous Reactivation of Clusters of X-Linked Genes Is Associated with the Plasticity of X-Inactivation in Mouse Trophoblast Stem Cells

Abstract

Random epigenetic silencing of the X-chromosome in somatic tissues of female mammals equalizes the dosage of X-linked genes between the sexes. Unlike this form of X-inactivation that is essentially irreversible, the imprinted inactivation of the paternal X, which characterizes mouse extra-embryonic tissues, appears highly unstable in the trophoblast giant cells of the placenta. Here, we wished to determine whether such instability is already present in placental progenitor cells prior to differentiation toward lineage-specific cell types. To this end, we analyzed the behavior of a GFP transgene on the paternal X both in vivo and in trophoblast stem (TS) cells derived from the trophectoderm of XX GFP blastocysts. Using single-cell studies, we show that not only the GFP transgene but also a large number of endogenous genes on the paternal X are subject to orchestrated cycles of reactivation/de novo inactivation in placental progenitor cells. This reversal of silencing is associated with local losses of histone H3 lysine 27 trimethylation extending over several adjacent genes and with the topological relocation of the hypomethylated loci outside of the nuclear compartment of the inactive X. The "reactivated" state is maintained through several cell divisions. Our study suggests that this type of "metastable epigenetic" states may underlie the plasticity of TS cells and predispose specific genes to relaxed regulation in specific subtypes of placental cells.

Lineage-specific regulation of imprinted X inactivation in extraembryonic endoderm stem cells

“…Studies of developing embryos or trophoblast stem (TS) cells derived from the TE [12] have revealed that, similarly to the randomly inactivated X, the inactive Xp in the TE lineage is associated with Xist ncRNA coating, depletion of active epigenetic marks and enrichment for the repressive H4K20me1 mark, the PRC2-dependent H3K27me3 mark and hypermethylation of CpG islands [3,13-18]. Despite these cumulative regulatory locks ensuring the maintenance of Xp silencing, the inactive state in the TE seems to be less stable than that of adult somatic tissues because transient reactivation of some Xp-linked genes occurs spontaneously in both TS and TE cells [18]. As a corollary, a large number of X-linked genes are expressed from both X chromosomes in female TS cells [13].…”

Developmental regulation of X-chromosome inactivation

“…Nevertheless, imprinted XCI seems to be less strictly controlled in the placenta than random XCI in the embryo. X--linked genes can get spontaneously reactivated in trophoblast giant cells in vivo [31,32] and also in trophoblast stem cells in vitro [33], in which imprinted XCI can even be transiently completely reversed [34]. The reason for this infidelity in silencing could be the unusual chromatin state of the Xp in extraembryonic tissues, which consists both of repressive as well as active chromatin marks [32] and shows less involvement of DNA--methylation, when compared to random XCI [35].…”

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

“…However, a number of X-linked diseases are not caused by hereditary, but rather, spontaneous rare mutations in exon region, leading to disease [214]. These mutations can cause missense, nonsense or frame-shift mutations.…”