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Significance The long noncoding Xist RNA coats and silences one X chromosome in female cells. How Xist localizes in cis to the inactive X compartment is not clear. Here, we reveal a required interaction between CIZ1 protein and Xist Repeat E motifs. Stochastic optical reconstruction microscopy (STORM) shows a tight association of CIZ1 with Xist RNA at the single-molecule level. Deletion of either CIZ1 or Repeat E causes dispersal of Xist RNA throughout the nucleoplasm, as well as loss of the heterochromatin mark H3K27me3 from the inactive X chromosome. We have thus identified a critical factor for stable association of Xist RNA with the inactive X chromosome.

Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1)