Evidence for Local Regulatory Control of Escape from Imprinted X Chromosome Inactivation

Abstract

X chromosome inactivation (XCI) is an epigenetic process that almost completely inactivates one of two X chromosomes in somatic cells of mammalian females. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophoblast stem (TS) cells, we address whether particular chromosomal interactions facilitate escape from imprinted XCI. We demonstrate that promoters of genes escaping XCI do not congregate to any particular region of the genome in TS cells. Further, the escape status of a gene was uncorrelated with the types of genomic features and gene activity located in contacted regions. Our results suggest that genes escaping imprinted XCI do so by using the same regulatory sequences as their expressed alleles on the active X chromosome. We suggest a model where regulatory control of escape from imprinted XCI is mediated by genomic elements located in close linear proximity to escaping genes.T HE three-dimensional shape of chromosomes has a direct impact upon gene regulation, as chromatin looping mediates the interaction of enhancers with transcriptional start sites (TSSs) (Lieberman-Aiden et al. 2009;Li and Reinberg 2011;Krivega and Dean 2012). Analysis of genome-wide interactions suggests that chromosomes self-organize into topologically associated domains (TADs) that are 0.8-1 Mb in linear length (Dixon et al. 2012). Loci within a TAD are more likely to interact with each other as opposed to forming interactions with loci residing in other TADs.Chromosomal interactions are thought to play a pivotal role in the epigenetic process of X chromosome inactivation (XCI) (Splinter et al. 2011). During XCI, mammalian females transcriptionally inactivate one X chromosome (Xi) per somatic cell to balance X-linked gene dosage with males (Chow and Heard 2009). Whereas genes on the active X chromosome (Xa) are thought to form stable interactions with other loci on the Xa (cis) and other chromosomes (trans), the interactions formed by Xi-linked loci are relatively less established, suggesting that Xi chromatin folds in a random manner (Splinter et al. 2011).In the mouse, two forms of XCI are observed: imprinted XCI and random XCI. Imprinted XCI occurs within extra-embryonic tissues and is characterized by the exclusive inactivation of the paternally derived X chromosome (Xp) (Takagi and Sasaki 1975). Random XCI occurs within somatic tissues of the developing embryo and adult (Lyon 1961). While imprinted and random XCI may initiate via distinct mechanisms (Kalantry et al. 2009), the genetic programs required for the maintenance of both forms appear similar (Marahrens et al. 1997;Kalantry et al. 2006;Jonkers et al. 2009; Shin et al. 2010).Interestingly, a few genes are known to escape both imprinted and random XCI and are expressed from both X chromosomes (Berletch et al. 2011;. Profiles of XCI escape vary among different cell types; the number of escape genes, termed escapers, ranges from 3% to 25% of all X-linked genes (Berletch et al. 2011 To date, no study has c...

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

“…The Xi is a complex epigenomic landscape that includes genes capable of escaping XCI (Carrel and Willard, 2005;Li and Carrel, 2008;Yang et al, 2010;Calabrese et al, 2012;Pinter et al, 2012;Mugford et al, 2014). Allele-specific ChIP-seq of mouse trophoblast stem cells (TSC) previously showed that the majority of CTCF binding sites on the imprinted paternal Xi is shared with the active maternal Xa (Calabrese et al, 2012), and that no specific structural features were discernible for genes that escape XCI (Mugford et al, 2014).…”

“…Allele-specific ChIP-seq of mouse trophoblast stem cells (TSC) previously showed that the majority of CTCF binding sites on the imprinted paternal Xi is shared with the active maternal Xa (Calabrese et al, 2012), and that no specific structural features were discernible for genes that escape XCI (Mugford et al, 2014). Here we carried out allele-specific ChIP-seq (Fig.…”

“…Meriting future investigation as well are the allele-specific binding patterns of CTCF to the Xa and Xi (Fig. 3), as CTCF-RNA interactions near escapee genes may facilitate the genes’ continued expression within facultative heterochromatin (Filippova et al, 2005;Li and Carrel, 2008;Calabrese et al, 2012;Mugford et al, 2014). …”

You are what you eat

“…Consequently, because the Xp is silenced, at least a functional maternal Ogt allele seems required in extra-embryonic tissues for proper preimplantation development. Surprisingly though, other studies have shown that Ogt does not systematically undergo normal iXCI in extra-embryonic tissues and have therefore defined Ogt as an iXCI-escaping gene in mouse trophoblastic stem cells [28–31]. Thus, female placentas sometimes have higher levels of OGT and O- GlcNAcylated proteins than male placentas [32**].…”

X marks the spot: Does it matter that O-GlcNAc Transferase is an X-linked gene?

“…Surprising though, more recent studies have shown that Ogt expression does not undergo normal iXCI in extraembryonic tissues. Indeed, a number of recent studies have identified Ogt as an iXCI-escaping gene in mouse trophoblast stem cells [51,52,53,54], suggesting that Ogt is never subjected to iXCI in extraembryonic tissues. Accordingly, biallelic expression of Ogt is detected in female mouse trophobast stem cells [51,53].…”