Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.

Ava C Carter ,Jin Xu,Meagan Y Nakamoto,Ankit Salhotra,Anil Mistry,Yuning Wei,Quanming Shi,Rui Li,Paul A Khavari ,Diana R Dou ,Robert T Batey ,Michael T Longaker ,Seung Woo Cho ,Kathryn E Yost ,James P Broughton ,Ryan C Ransom ,Deborah S Wuttke ,Brian Zarnegar ,Surya Nagaraja ,Howard Y Chang

doi:10.7554/elife.54508

Abstract

The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss 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 silencing. 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.

Highlights

Xist is a 17kb long noncoding RNA that acts through specific interactions between its distinct RNA domains and nuclear effector proteins
In two independent Spen KO mouse embryonic stem cells (mESCs) clones, we found no X chromosome site that is reproducibly silenced upon Xist induction, suggesting that Spen is absolutely required for gene silencing at the level of chromatin accessibility (Extended Data Figure 1b)
We show that Spen, a highly conserved and pleiotropic RNA-binding protein, binds to and regulates specific classes of endogenous retrovirus K (ERVK) loci in mouse embryonic stem cells

Summary

Introduction

Xist is a 17kb long noncoding RNA that acts through specific interactions between its distinct RNA domains and nuclear effector proteins. The Xist RNA-associated protein complex was identified in 2015 using both genetic and affinity-based methods, and consists of multiple pleiotropic proteins, many of which are highly conserved throughout evolution and act on chromatin structure and gene regulation in myriad systems[3,4,5,6,7]. This suggests that Xist evolved the ability to bind these proteins in the eutherian mammals, coopting those which evolved initially to perform other epigenetic functions. Understanding how the Xist RNA sequence was evolutionarily stitched together from these existing building blocks to gain protein-binding potential is of great interest towards understanding dosage compensation and lncRNA-mediated gene regulation genome-wide

Methods

Results

Conclusion