Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression

Andrea Cerase,Alexander N Young,Monica Di Giacomo,Andreas Buness,Andreas Hierholzer,Nerea Blanes Ruiz,Michela Ascolani,Mirjam Arnold,Giuseppe Trigiante,Manish Kumar,Sarah J Marzi,Philip Avner,Gabrielle M Sant

doi:10.1038/s42003-021-01945-1

Abstract

Female mammals achieve dosage compensation by inactivating one of their two X chromosomes during development, a process entirely dependent on Xist, an X-linked long non-coding RNA (lncRNA). At the onset of X chromosome inactivation (XCI), Xist is up-regulated and spreads along the future inactive X chromosome. Contextually, it recruits repressive histone and DNA modifiers that transcriptionally silence the X chromosome. Xist regulation is tightly coupled to differentiation and its expression is under the control of both pluripotency and epigenetic factors. Recent evidence has suggested that chromatin remodelers accumulate at the X Inactivation Center (XIC) and here we demonstrate a new role for Chd8 in Xist regulation in differentiating ES cells, linked to its control and prevention of spurious transcription factor interactions occurring within Xist regulatory regions. Our findings have a broader relevance, in the context of complex, developmentally-regulated gene expression.

Highlights

Female mammals achieve dosage compensation by inactivating one of their two X chromosomes during development, a process entirely dependent on Xist, an X-linked long noncoding RNA
In order to assess the efficiency of X chromosome inactivation initiation, we differentiated these cells from 2i conditions to the neuronal progenitor cell state (NPCs) for 3 days
Whilst many aspects of Xist regulation have been intensely studied over the years[17,18,19,20,21,22,23,24,62], little is known about the role of chromatin remodelers in the context of X chromosome inactivation (XCI)

Summary

Introduction

Female mammals achieve dosage compensation by inactivating one of their two X chromosomes during development, a process entirely dependent on Xist, an X-linked long noncoding RNA (lncRNA). In mammals there are about 30 different types of ATP-dependent chromatin remodelers, belonging to four major remodeler families[32]: SWI/SNF, ISWI, NURD-CHD, and INO80 Such complexes are implicated in most cell activities, from regulation of differentiation, to pluripotency and gene-specific activities. In order to focus our analysis on chromatin remodelers likely involved in the regulation of the initiation of XCI, we screened for candidate regulators, using the following criteria: (i) accumulation and binding to the X inactivation centre (XIC)[28,36]; (ii) robust expression during early mouse developmental stages[37,38]; (iii) a KO phenotype, where known, compatible with a role in XCI (MGI, www.informatics.jax.org/) or phenocopying XCI-defects Based on these selection criteria and preliminary analysis, we decided to focus our immediate attention on the ChromodomainHelicase-DNA-binding protein 8 (Chd8), which belongs to the CHD family. Chd[8] regulates strong yet controlled bursts of Xist expression, which are necessary for its correct spreading across the chromatin and initiation of XCI by preventing the spurious binding of TFs at the Xist promoter

Methods

Results

Conclusion