The X as model for RNA's niche in epigenomic regulation

Abstract

The X-linked region now known as the "X-inactivation center" (Xic) was once dominated by protein-coding genes but, with the rise of Eutherian mammals some 150-200 million years ago, became infiltrated by genes that produce long noncoding RNA (ncRNA). Some of the noncoding genes have been shown to play crucial roles during X-chromosome inactivation (XCI), including the targeting of chromatin modifiers to the X. The rapid establishment of ncRNA hints at a possible preference for long transcripts in some aspects of epigenetic regulation. This article discusses the role of RNA in XCI and considers the advantages RNA offers in delivering allelic, cis-limited, and locus-specific control. Unlike proteins and small RNAs, long ncRNAs are tethered to the site of transcription and effectively tag the allele of origin. Furthermore, long ncRNAs are drawn from larger sequence space than proteins and can mark a unique region in a complex genome. Thus, like their small RNA cousins, long ncRNAs may emerge as versatile and powerful regulators of the epigenome.

Figure 1.

The X-inactivation center, its noncoding genes, and their functions during the XCI cascade. (A) More than seven noncoding genes have been found within or around the Xic. Xist, RepA, Tsix, and Xite have ascribed function. The regions responsible for X-chromosome pairing, counting/choice, and spreading/silencing are indicated. (B) Steps of XCI and the factors known to regulate them.

Figure 2.

Yin-Yang relationship between Tsix and Xist RNAs. Tsix bears a critical relationship to Xist expression. In undifferentiated cells (pre-XCI), Tsix is expressed from both Xs at high levels and Xist RNA is expressed at low basal levels (∼5 copies). At the onset of cell differentiation, Tsix persists only on the chromosome selected to become Xa. It is the persistence of Tsix RNA that prevents the up-regulation of Xist on Xa. Conversely, the down-regulation of Tsix on Xi creates a permissive state for Xist transactivation and spread of the RNA along the X to initiate chromosome-wide silencing. Tsix is eventually turned off on Xa once the pattern of XCI is fixed.

Figure 3.

Symmetry break mediated by pairing and Tsix. Adapted from (Anguera et al. 2006) and (Lee 2009): In the pre-XCI state, the Xs are epigenetically equivalent, both expressing Tsix at high levels and Xist at low basal levels. Falling levels of Oct4 during cell differentiation triggers X-X pairing. Pairing is mediated by Ctcf, Tsix, and Xite and enables cross-talk to achieve correct counting and mutually exclusive Xa and Xi fates. Transcription factors such as Ctcf, Oct4, and others (red, green circles), which were previously randomly distributed between the two Xs, shift to bind one X, a state that is thermodynamically favored. The chromosome that retains the transcription factors maintains Tsix expression and becomes Xa. Loss of factor binding on the future Xi enables RepA to target PRC2 and H3-K27me3 to the 5′ end of Xist, an event that leads to Xist‘s transcriptional activation. Xist RNA spreads along the future Xi and recruits PRC2 to it to initiate chromosome-wide silencing.

Figure 4.

Long ncRNAs recruit chromatin modifiers in a cis-limited and locus-specific manner. The example of PRC2 recruitment by RepA RNA is shown.