Functional analysis of the highly conserved exon IV of XIST RNA

X inactivation is effected by a large CIS-acting RNA molecule termed the X inactive specific transcript (XIST). Exon IV of XIST RNA is highly conserved at the primary sequence level and is predicted to form a stable stem-loop structure. These features suggest that it is important for XIST RNA function. We have used homologous recombination to delete exon IV of the mouse XIST gene. Surprisingly we found no detectable effects on X inactivation. Heterozygous female animals show normal random X inactivation and transcripts from the mutant allele were seen to localise IN CIS over the length of the inactive X chromosome. There was however a reduced steady state level of mutant relative to wild type XIST RNA. This effect was not attributable to decreased stability, suggesting that the deletion affects transcription or processing of XIST RNA.