Identification of regulatory elements flanking human XIST reveals species differences

BACKGROUND: The transcriptional silencing of one X chromosome in eutherians requires transcription of the long non-coding RNA gene, XIST. Many regulatory elements have been identified downstream of the mouse Xist gene, including the antisense Tsix gene. However, these elements do not show sequence conservation with humans, and the human TSIX gene shows critical differences from the mouse. Thus we have undertaken an unbiased identification of regulatory elements both downstream and upstream of the human XIST gene using DNase I hypersensitivity mapping. RESULTS: Downstream of XIST a single DNase I hypersensitive site was identified in a mouse undifferentiated ES cell line containing an integration of the human XIC region. This site was not observed in somatic cells. Upstream of XIST, the distance to the flanking JPX gene is expanded in humans relative to mice, and we observe a hypersensitive site 65 kb upstream of XIST, in addition to hypersensitive sites near the XIST promoter. This -65 region has bi-directional promoter activity and shows sequence conservation in non-rodent eutheria. CONCLUSIONS: The lack of regulatory elements corresponding to human TSIX lends further support to the argument that TSIX is not a regulator of XIST in humans. The upstream hypersensitive sites we identify show sequence conservation with other eutheria, but not with mice. Therefore the regulation of XIST seems to be different between mice and man, and regulatory sequences upstream of XIST may be important regulators of XIST in non-rodent eutheria instead of Tsix which is critical for Xist regulation in rodents.