Abstract
To ensure dosage compensation between the sexes, one randomly chosen X chromosome is silenced in each female cell in the process of X-chromosome inactivation (XCI). XCI is initiated during early development through upregulation of the long non-coding RNA Xist, which mediates chromosome-wide gene silencing. Cell differentiation, Xist upregulation and gene silencing are thought to be coupled at multiple levels to ensure inactivation of exactly one out of two X chromosomes. Here we perform an integrated analysis of all three processes through allele-specific single-cell RNA-sequencing. Specifically, we assess the onset of random XCI in differentiating mouse embryonic stem cells, and develop dedicated analysis approaches. By exploiting the inter-cellular heterogeneity of XCI onset, we identify putative Xist regulators. Moreover, we show that transient Xist upregulation from both X chromosomes results in biallelic gene silencing right before transitioning to the monoallelic state, confirming a prediction of the stochastic model of XCI. Finally, we show that genetic variation modulates the XCI process at multiple levels, providing a potential explanation for the long-known X-controlling element (Xce) effect, which leads to preferential inactivation of a specific X chromosome in inter-strain crosses. We thus draw a detailed picture of the different levels of regulation that govern the initiation of XCI. The experimental and computational strategies we have developed here will allow us to profile random XCI in more physiological contexts, including primary human cells in vivo.
Highlights
To ensure dosage compensation between the sexes, one randomly chosen X chromosome is silenced in each female cell in the process of X-chromosome inactivation (XCI)
By adapting single-cell transcriptome analysis approaches, including recently developed concepts like RNA velocity, to an AS process such as random XCI, we could draw a detailed picture of the different steps occurring at the onset of X inactivation
In this way we were able to answer several open questions by (1) dissecting the dynamics of XCI along developmental progression with allelic resolution and (2) quantifying the expression heterogeneity of the main genes involved in the XCI process, their regulatory relationships and their dynamics
Summary
To ensure dosage compensation between the sexes, one randomly chosen X chromosome is silenced in each female cell in the process of X-chromosome inactivation (XCI). Gene dosage differences between the sexes for X-linked genes are mostly compensated through X-chromosome inactivation (XCI) In this process, each female cell will silence one randomly chosen X chromosome in a cell-autonomous fashion[1]. XCI is established during early embryonic development in a complex multi-step process It is initiated by upregulation of the long non-coding RNA Xist, the master regulator of XCI1. The current model is that Xist is initially upregulated independently on each chromosome in a random fashion and that establishment of a MA state is ensured through negative feedback regulation[2] This feedback is thought to be mediated by silencing of an essential X-linked Xist activator[9,10]. It remains unknown which factors trigger Xist upregulation in the endogenous context and whether this is mediated through modulating the activity of other Xist regulators such as Rnf[12] or Tsix
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
