Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Abstract

X chromosome inactivation (XCI) is an essential epigenetic process which involves several non-coding RNAs (ncRNAs), including Xist, the master regulator of X-inactivation initiation. Xist is flanked in its 5' region by a large heterochromatic hotspot, which contains several transcription units including a gene of unknown function, Ftx (five prime to Xist). In this article, we describe the characterization and functional analysis of murine Ftx. We present evidence that Ftx produces a conserved functional long ncRNA, and additionally hosts microRNAs (miR) in its introns. Strikingly, Ftx partially escapes X-inactivation and is upregulated specifically in female ES cells at the onset of X-inactivation, an expression profile which closely follows that of Xist. We generated Ftx null ES cells to address the function of this gene. In these cells, only local changes in chromatin marks are detected within the hotspot, indicating that Ftx is not involved in the global maintenance of the heterochromatic structure of this region. The Ftx mutation, however, results in widespread alteration of transcript levels within the X-inactivation center (Xic) and particularly important decreases in Xist RNA levels, which were correlated with increased DNA methylation at the Xist CpG island. Altogether our results indicate that Ftx is a positive regulator of Xist and lead us to propose that Ftx is a novel ncRNA involved in XCI.

Nonrandom X Chromosome Inactivation Is Influenced by Multiple Regions on the Murine X Chromosome

“…This is consistent with the proposal that "only one locus is involved" in Xce if Xce acts upon the XCI process vs. cell selection (Cattanach and Williams 1972). With the recent identification of numerous X-linked genes and genetic elements that contribute to the XCI process and uncovering the stochastic nature of this process (Monkhorst et al 2008;Jonkers et al 2009;Tian et al 2010;Chureau et al 2011;Pontier and Gribnau 2011;Nora et al 2012); however, the number and diversity of loci that define Xce may be more complex than originally envisioned and vary with the relatedness of the X chromosomes being evaluated.…”

“…Recently identified elements within the broad Xic candidate region have been shown to affect XCI by affecting choice. Distal to Xist, the noncoding genes Jpx and Ftx and the protein-coding gene Rnf12 have been shown to influence XCI by affecting Xist expression (Jonkers et al 2009;Tian et al 2010;Chureau et al 2011;Pontier and Gribnau 2011) (Figure 5A). SNPs in any of these genes may contribute to the loss of skewing observed in progeny of the RX2-derived male 1114m.…”

Systematic Mapping of RNA-Chromatin Interactions In Vivo

“…More specifically, H9 and HEK share XIST involvement in heterochromatin, but XIST also attaches to less compact parts of the X chromosome through protein bridges specifically in HEK cells. If this was the case, we would anticipate to see differences in diRNA activities on XIST associated lincRNAs TSIX [18,19] and FTX [20] between HEK and H9 cells. The two lincRNAs exhibited similar degrees of pxRNA activities between HEK and H9 ( Figure S4A-B), consistent with the observed XIST pxRNA activities and reported XCI in H9 cells [13].…”

Interplay of chromatin modifications and non-coding RNAs in the heart

“…88 FISH has traditionally been the method of choice to study long ncRNA dependent-chromatin interactions. 89,90 More recently, FISH was employed to assay changes in chromatin architecture for KCNQ1OT1 a lncRNA that regulates KCNQ1 expression in the developing heart. 91 Alternatively, locus-specific lncRNA interactions can be examined using formaldehyde fixation and chromatin immunoprecipitation methods (RNA-ChIP) that use antibodies that recognize RNA-binding proteins such as EZH2 and G9A.…”