Journal Article

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

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

2020

Overview

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. The genetic material inside cells is often packaged into thread-like structures called chromosomes. In humans, mice and other mammals, a pair of sex chromosomes determines the genetic or chromosomal sex of each individual. Those who inherit two “X” chromosomes are said to be chromosomally female, while chromosomal males have one “X” and one “Y” chromosome. This means females have twice as many copies of genes on the X chromosome as a male does, which turns out to be double the number that the body needs. To solve this problem, mammals have developed a strategy known as dosage compensation. The second X chromosome in females becomes “silent”: its DNA remains unchanged, but none of the genes are active. A long noncoding RNA molecule called Xist is responsible for switching off the extra X genes in female cells. It does this by coating the entirety of the second X chromosome. Normally, RNA molecules transmit the coded instructions in genes to the cellular machinery that manufactures proteins. “Noncoding” RNAs like Xist, however, are RNAs that have taken on different jobs inside the cell. Researchers believe that the ancestral Xist gene may have once encoded a protein but changed over time to produce only a noncoding RNA. Carter, Xu et al. therefore set out to find out how exactly this might have happened, and also how Xist might have acquired its ability to switch genes off. Initial experiments used mouse cells grown in the laboratory, in which a protein called Spen was deleted. Spen is known to help Xist silence the X chromosome. In female cells lacking Spen, the second X chromosome remained active. Other chromosomes in male and female cells also had stretches of DNA that became active upon Spen’s removal. These DNA sequences, termed endogenous retroviruses, were remnants of ancestral viral infections. In other words, Spen normally acted as an antiviral defense. Analysis of genetic sequences showed that Spen recognized endogenous retrovirus sequences resembling a key region in Xist, a region which was needed for Xist to work properly. Inserting fragments of endogenous retroviruses into a defective version of Xist lacking this region also partially restored its ability to inactivate genes, suggesting that X chromosome silencing might work by hijacking cellular defenses against viruses. That is, female cells essentially ‘pretend’ there is a viral infection on the second X chromosome by coating it with Xist (which mimics endogenous retroviruses), thus directing Spen to shut it down. This research is an important step towards understanding how female cells carry out dosage compensation in mammals. More broadly, it sheds new light on how ancient viruses may have shaped the evolution of noncoding RNAs in the human genome.

• Publisher: eLife Science Publications, Ltd,eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Animal experimentation / Animals / Antisense RNA / Antiviral drugs / Binding Sites / Cell Line / Chromatin / Chromosomes / Chromosomes and Gene Expression / Cloning / DNA / DNA sequencing / DNA-Binding Proteins - genetics / DNA-Binding Proteins - metabolism / Dosage compensation / Dosage Compensation, Genetic / Embryo cells / Embryonic stem cells / Endogenous Retroviruses - genetics / Endogenous Retroviruses - metabolism / epigenetic / Evolutionary biology / Female / Gene silencing / Genes / Genetic engineering / Genetic research / Genomes / Genomics / Host-Pathogen Interactions / Intelligence gathering / long noncoding RNA / Mice / Mouse Embryonic Stem Cells - metabolism / Mouse Embryonic Stem Cells - virology / Ontology / Protein Binding / Protein interaction / Proteins / Retroviruses / Ribonucleic acid / RNA / RNA, Long Noncoding - genetics / RNA, Long Noncoding - metabolism / RNA, Viral - genetics / RNA, Viral - metabolism / RNA-Binding Proteins - genetics / RNA-Binding Proteins - metabolism / RNA-mediated interference / RNA-protein interactions / Silence / Stem cell transplantation / Stem cells / Time / Transcription / Transcription (Genetics) / transposon / Transposons / Virus diseases / X Chromosome / X Chromosome Inactivation / X chromosomes / Xist