New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency

Abstract

Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.

Keywords: TAD; XCI; XCR; Xist; chromatin; embryo development; epigenetics; gene regulation; polycombs; reprogramming.

Figure 1

X-chromosome inactivation (XCI) in placental mammals (a) Xist RNA clouds shown by RNA fluorescence in-situ hybridization (FISH) on mouse female fibroblasts. Reproduced with permission from [70]. scale bar = 2 µm (b) Schematic representation of chromatin changes accompanying X-chromosome inactivation (XCI). Active X chromosomes (Xas) are shown in green. The inactive X chromosome (Xi) is shown in red. Ac: acetylation; Me3: H3K27me3; Ub: H2AK119ub1. PTM: post-translational modifications.

Figure 2

X-chromosome reactivation (XCR) during induced pluripotent stem cell (iPSC) reprogramming followed by X chromosome aneuploidy. (a) Roadmap showing XCR during mouse embryonic fibroblast reprogramming to iPSC by Oct4, Sox2, Klf4 and c-Myc factors; (b) XCR followed by rapid loss of X chromosome or X chromosome aneuploidy in XaXa iPSCs.

Figure 3

Genome organization. The mammalian genome possesses different levels of organization. From a large scale to a fine scale, chromosome territories (each in a different color), compartments A (active chromatin) and B (repressed chromatin), topologically associated domains (TADs), and nucleosomes of two homologous alleles are shown (from left to right). Middle: Compartments A and B are indicated by a green and red background, respectively. Homologous alleles are regulated independently.

Figure 4

Gaps in our knowledge of XCR. Several unanswered questions during X-chromosome reactivations during reprogramming to pluripotent stem cell from somatic cell and also during germline development are depicted.