Tissue-Specific and NF-kappaB-Independent Xist RNA Localization Patterns in Female Intestinal, Blood, and Muscle Progenitors

X-Chromosome Inactivation (XCI), driven by the expression of Xist RNA and the enrichment of various repressive epigenetic marks, results in the formation of a mostly inactive X chromosome (Xi) to equalize X-linked gene expression between sexes. Unexpectedly, in unstimulated female lymphocytes that are largely quiescent, these epigenetic features are largely absent but are restored by NF-κB signaling following their activation. To determine whether these epigenetic phenotypes correlate with quiescence or NF-κB activation in other tissues, we evaluated female progenitor and stem cells from intestine, blood, and muscle. Despite known NF-κB activation, intestinal progenitors have variable Xist RNA patterns, whereas blood progenitors and neutrophils show a strong correlation between NF-κB activation status and Xist RNA localization. In contrast, muscle satellite cells (SCs) and myoblasts exhibit Xist RNA accumulation at the Xi without NF-κB activation. Xist RNA localization patterns in SCs change with age, yet adult SCs have an Xi that is mostly transcriptionally silent while allowing expression of muscle-specific X-linked genes including Dmd . These findings reveal that female somatic cells employ diverse, tissue-specific epigenetic mechanisms to maintain X chromosome inactivation, enabling cell type specific Xi gene expression while preserving chromosome-wide silencing.