RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes

• Published in: The EMBO journal 2021-12, Vol.40 (24), p.e105862-n/a
• Main Authors: Enervald, Elin, Powell, Lynn Marie, Boteva, Lora, Foti, Rossana, Blanes Ruiz, Nerea, Kibar, Gözde, Piszczek, Agnieszka, Cavaleri, Fatima, Vingron, Martin, Cerase, Andrea, Buonomo, Sara B C
• Format: Article
• Language: English
• Subjects: Animals; Asymmetry; Binding; Cell Differentiation; Cell Line; Chromatin; Chromosomes; Deactivation; Differentiation; EMBO09; EMBO11; Embryo cells; Female; Gene expression; Identities; Inactivation; KAP1; Mice; Mouse Embryonic Stem Cells - cytology; Promoter Regions, Genetic; Promoters; Ribonucleic acid; RIF1; RNA; RNA, Long Noncoding - genetics; Stem cell transplantation; Stem cells; Stochastic Processes; Stochasticity; Telomere-Binding Proteins - metabolism; Transcription; Tripartite Motif-Containing Protein 28 - metabolism; Tsix; Up-Regulation; X Chromosome Inactivation; X chromosomes; Xist
• ISSN: 0261-4189; 1460-2075
• DOI: 10.15252/embj.2020105862

The onset of random X chromosome inactivation in mouse requires the switch from a symmetric to an asymmetric state, where the identities of the future inactive and active X chromosomes are assigned. This process is known as X chromosome choice. Here, we show that RIF1 and KAP1 are two fundamental factors for the definition of this transcriptional asymmetry. We found that at the onset of differentiation of mouse embryonic stem cells (mESCs), biallelic up‐regulation of the long non‐coding RNA Tsix weakens the symmetric association of RIF1 with the Xist promoter. The Xist allele maintaining the association with RIF1 goes on to up‐regulate Xist RNA expression in a RIF1‐dependent manner. Conversely, the promoter that loses RIF1 gains binding of KAP1, and KAP1 is required for the increase in Tsix levels preceding the choice. We propose that the mutual exclusion of Tsix and RIF1, and of RIF1 and KAP1, at the Xist promoters establish a self‐sustaining loop that transforms an initially stochastic event into a stably inherited asymmetric X‐chromosome state. SYNOPSIS Random X chromosome inactivation regulated by Xist and Tsix lncRNAs involves switching from a symmetric to an asymmetric state. Here, this process is shown to be differentially controlled by chromatin factors RIF1 and KAP1 in mouse embryonic stem cells. Tsix RNA levels increase at the onset of differentiation. Tsix RNA asymmetrically weakens RIF1 association with one Xist promoter. In the absence of RIF1, KAP1 gains access to one of the two Xist promoters/ Tsix terminators. KAP1 binding boosts the levels of Tsix, reinforcing RIF1 exclusion from the future active X chromosome. RIF1 marks the future inactive X chromosome by promoting in cis expression of Xist. Graphical Abstract Differentiation‐induced Tsix RNA triggers asymmetric distribution of RIF1 and KAP1 on the future inactive and active mouse X chromosomes, respectively, establishing a self‐sustaining Xist expression loop from an initially stochastic event.