A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced

TLDR

During early mammalian female development, one of the two X chromosomes becomes inactivated, and while Xist RNA coating initiates X inactivation, the mechanism by which this signal leads to transcriptional silencing remains poorly understood. The study aims to determine how Xist RNA creates a transcriptionally silent nuclear compartment and induces gene repression through A‑repeat‑dependent relocation of genes into this domain. Xist RNA functions by forming a transcriptionally silent compartment independent of its A‑repeats, while its A‑repeats drive the relocation of genes into this compartment to repress transcription. The authors found that Xist RNA‑coated X chromosomes exclude RNA Polymerase II and transcription factors early, before complete gene silencing, and that transcribed genes reside at the periphery or outside the Xist domain while silenced genes relocate inside a transcriptionally silent compartment that forms independently of the A‑repeats, though the A‑repeats are necessary for gene relocation into this domain.

Abstract

During early mammalian female development, one of the two X chromosomes becomes inactivated. Although X-chromosome coating by Xist RNA is essential for the initiation of X inactivation, little is known about how this signal is transformed into transcriptional silencing. Here we show that exclusion of RNA Polymerase II and transcription factors from the Xist RNA-coated X chromosome represents the earliest event following Xist RNA accumulation described so far in differentiating embryonic stem (ES) cells. Paradoxically, exclusion of the transcription machinery occurs before gene silencing is complete. However, examination of the three-dimensional organization of X-linked genes reveals that, when transcribed, they are always located at the periphery of, or outside, the Xist RNA domain, in contact with the transcription machinery. Upon silencing, genes shift to a more internal location, within the Xist RNA compartment devoid of transcription factors. Surprisingly, the appearance of this compartment is not dependent on the A-repeats of the Xist transcript, which are essential for gene silencing. However, the A-repeats are required for the relocation of genes into the Xist RNA silent domain. We propose that Xist RNA has multiple functions: A-repeat-independent creation of a transcriptionally silent nuclear compartment; and A-repeat-dependent induction of gene repression, which is associated with their translocation into this silent domain.