Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Abstract
The Xist lncRNA mediates X chromosome inactivation (XCI)1,2. Here we show that Spen, an Xist-binding repressor protein essential for XCI3-9, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing10-11. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
Data availability
All raw and processed sequencing data have been deposited in GEO under accession number GSE131413.
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Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivationNCBI Gene Expression Omnibus, GSE131413.
Article and author information
Author details
Funding
National Human Genome Research Institute (HG007735)
- Howard Y Chang
National Human Genome Research Institute (HG004361)
- Howard Y Chang
Scleroderma Research Foundation
- Howard Y Chang
Howard Hughes Medical Institute
- Howard Y Chang
National Institute of General Medical Sciences (GM120347)
- Robert T Batey
- Deborah S Wuttke
National Institute of Dental and Craniofacial Research (DEO26730)
- Michael T Longaker
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Gene W Yeo, University of California, San Diego, United States
Version history
- Received: December 17, 2019
- Accepted: May 5, 2020
- Accepted Manuscript published: May 7, 2020 (version 1)
- Version of Record published: June 9, 2020 (version 2)
Copyright
© 2020, Carter et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.