Aging activates, represses, and remodels the silent X chromosome and its escape across cell types of the female mouse hippocampus

Females show an advantage in lifespan and cognition in aging human populations. The X chromosome is a major source of sex difference, as female mammals harbor an inactive (Xi) and active (Xa) following X chromosome inactivation (XCI). Whether Xi – or the silent X – can activate in the aging brain and thus increase X dose is unknown. Here, we performed single nuclei RNA-sequencing in the young and aging hippocampus of female mice and applied allele-specific computational analysis. We show that aging remodels transcription of Xi and Xa across hippocampal cell types. Aging preferentially induced gene expression changes on the X chromosomes compared to the autosomes. Xi underwent activation and repression of select genes, particularly in dentate gyrus neurons, critical to learning and memory. Overall design: Female M. musculus XistloxP +/-,Zp3-cre mice with a congenic C57BL/6J background, were crossed with male M. castaneous mice. XX progeny carrying the XistloxP +/-, Zp3-cre allele were used for single nuclei RNA sequencing. The fresh hippocampi of four young (3-4 month) and four old (23-24 month) mice were dissected and frozen for downstream snRNAseq studies.