The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products

Abstract

Accumulation of the Xist long noncoding RNA (lncRNA) on one X chromosome is the trigger for X chromosome inactivation (XCI) in female mammals. Xist expression, which needs to be tightly controlled, involves a cis-acting region, the X-inactivation center (Xic), containing many lncRNA genes that evolved concomitantly to Xist from protein-coding ancestors through pseudogeneization and loss of coding potential. Here, we uncover an essential role for the Xic-linked noncoding gene Ftx in the regulation of Xist expression. We show that Ftx is required in cis to promote Xist transcriptional activation and establishment of XCI. Importantly, we demonstrate that this function depends on Ftx transcription and not on the RNA products. Our findings illustrate the multiplicity of layers operating in the establishment of XCI and highlight the diversity in the modus operandi of the noncoding players.

Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X‐Chromosome Inactivation

“…[ 75,76 ] Yet another Xist‐activating lncRNA, named Ftx, is located about 100 kb upstream of Xist (Figures 1 and 5a). [ 77,78 ] Ftx activates Xist in cis by the act of transcription, independent of its lncRNA and the microRNA cluster it contains, and can therefore not be one of the trans ‐acting xXA factors that have been predicted to underlie female specificity. [ 78 ] In conclusion, several positive X‐encoded regulators of Xist have been identified, but additional factors necessary to mediate female‐specific XCI onset remain to be found.…”

Mechanistic diversification of XIST regulatory network in mammals

“…We next analyzed the function of JPX transcripts as they were described as the major functional component in the mouse (Tian et al, 2010). We used an LNA-GapmeR (LGs)-mediated knockdown (KD) strategy ( Figure 2D) that have been previously used for the functional analysis of several 20 lncRNAs (Furlan et al, 2018;Leucci et al, 2016;Luo et al, 2016;Tripathi et al, 2010). To address JPX function in an embryonic context, we carried out this analysis in non-eroded primed female hESCs, with a percentage of XIST-expressing cells above 90% (Vallot et al, 2015).…”

“…Particularly relevant are the lncRNA genes hosted within the Xic, 30 which have been linked to Xist regulation in the mouse: Tsix and Linx acts as major repressor of Xist expression while Jpx and Ftx acts as positive regulators. The mechanistic dissection of these Xiclinked and other lncRNA loci highlighted that their molecular function is not only mediated by the RNA molecule itself, but may also involve various entities such the act of transcription or key regulatory elements embedded within their locus (Cho et al, 2018;Engreitz et al, 2016;Furlan et al, 2018;Paralkar et al, 2016). For instance, the antisense transcription of the Tsix gene over the Xist locus contributes to the monoallelic repression of Xist (Navarro et al, 2005); Tsix transcription is itself controlled by the upstream lncRNA gene, Linx (Giorgetti et al, 2014;Nora et al, 2012).…”

“…For instance, the antisense transcription of the Tsix gene over the Xist locus contributes to the monoallelic repression of Xist (Navarro et al, 2005); Tsix transcription is itself controlled by the upstream lncRNA gene, Linx (Giorgetti et al, 2014;Nora et al, 2012). Ftx transcription has been shown to be essential for Xist expression cis (Furlan et al, 2018) while Jpx was proposed to act through its RNA molecule by binding and titrating away the CTCF protein from 5…”

“…The antagonistic action of the Xic-linked LRGs is likely facilitated by the spatial segregation of the Xist-and Tsixassociated regulators in two adjacent and oppositely regulated topologically associated domains (TADs) (Nora et al, 2012). These TADs also delimit internal long-range interactions to ensure 10 contacts between regulatory elements and their target genes; intra-TAD interactions have been described between the Xist and Ftx LRGs and between Tsix promoter and Linx LRG (Furlan et al, 2018;Nora et al, 2012).…”