Higher order chromatin structure at the X-inactivation center via looping DNA

Abstract

In mammals, the silencing step of the X-chromosome inactivation (XCI) process is initiated by the non-coding Xist RNA. Xist is known to be controlled by the non-coding Xite and Tsix loci, but the mechanisms by which Tsix and Xite regulate Xist are yet to be fully elucidated. Here, we examine the role of higher order chromatin structure across the 100-kb region of the mouse X-inactivation center (Xic) and map domains of specialized chromatin in vivo. By hypersensitive site mapping and chromosome conformation capture (3C), we identify two domains of higher order chromatin structure. Xite makes looping interactions with Tsix, while Xist makes contacts with Jpx/Enox, another non-coding gene not previously implicated in XCI. These regions interact in a developmentally-specific and sex-specific manner that is consistent with a regulatory role in XCI. We propose that dynamic changes in three-dimensional architecture leads to formation of separate chromatin hubs in Tsix and Xist that together regulate the initiation of X-chromosome inactivation.

A Boundary Element BetweenTsixandXistBinds the Chromatin Insulator Ctcf and Contributes to Initiation of X-Chromosome Inactivation

“…By contrast, the 81-bp RS14d has 86% identity between mouse and human sequences and 80% identity between mouse and bovine sequences. RS14d coincides with a strong DNase I hypersensitive site (Tsai et al 2008).…”

“…It was also shown that ACH-1 and ACH-2 are separated by a chromatin transitional zone located at the 39 terminus of Xist ( Figure 1A) (Tsai et al 2008), which was proposed to buffer opposing chromatin forces between the Tsix-and the Xist-centered domains. How this region does so is not known, but the 39 end of Xist has a number of noteworthy features, including a strong DNase I hypersensitive site (Tsai et al 2008).…”

“…Xite lies upstream of Tsix and positively regulates the antisense RNA (Ogawa and Lee 2003;Stavropoulos et al 2005). Jpx/Enox resides upstream of Xist (Chureau et al 2002;Johnston et al 2002), makes looping contacts with Xist (Tsai et al 2008), and has recently been shown to activate Xist expression (Tian et al 2010).…”

“…A recent study has revealed a series of complex threedimensional interactions underlying the genetic interactions between the noncoding genes (Tsai et al 2008). It is proposed that the Xic is partitioned into two active chromatin hubs (ACHs) ( Figure 1A)-permissive higher-order structures within which looping interactions between genes facilitate developmentally specific chromatin interactions (Tolhuis et al 2002;Kosak and Groudine 2004;Splinter et al 2006).…”

“…How this region does so is not known, but the 39 end of Xist has a number of noteworthy features, including a strong DNase I hypersensitive site (Tsai et al 2008). Previously thought to terminate in exon 7 (formerly exon 6), Xist is now known to extend 3 kb to include a small eighth exon (Brockdorff et al 1992;Hong et al 1999).…”