Role of the region 3′ to Xist exon 6 in the counting process of X-chromosome inactivation

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Abstract
During early embryogenesis of female mammals, one of the two X chromosomes is randomly chosen to be inactivated in each cell1, leading to the transcriptional silencing of thousands of genes on this chromosome. This random X-inactivation process also occurs during in vitro differentiation of female embryonic stem (ES) cells2,3,4. A locus on the X chromosome, the X inactivation centre (Xic) is initially 'counted', given that at least two copies of Xic must be present per diploid genome in order for inactivation to occur2. The counting process ensures that one X chromosome remains active in diploid cells. In the mouse, the essential functions of Xic can be assured by a 450-kb region5,6 containing the Xist gene. Xist maps within Xic (refs 7, 8, 9, 10) and is necessary in cis for inactivation11,12. The Xist transcript is a 15-kb RNA which is confined within the nucleus and coats the inactive X chromosome13. In order to characterize functional elements within Xic and the Xist gene, we created a 65-kb cre/loxP deletion extending 3′ to Xist exon 6. In undifferentiated ES cells, Xist expression from the deleted X chromosome was markedly reduced. In differentiated XX ES cells containing one deleted X chromosome, the X inactivation process still occurred but was never initiated from the unmutated X chromosome. In differentiated ES cells that were essentially XO, the mutated Xic was capable of initiating X inactivation, even in the absence of another Xic. These results demonstrate a role for the region 3′ to Xist exon 6 in the counting process and suggest that counting is mediated by a repressive mechanism which prevents inactivation of a single X chromosome in diploid cells.