How Maternal X Chromosome Skew Accelerates Brain Aging

X Chromosome InactivationX Chromosome Inactivation

Most mammals follow an XY sex-determination system: females have two X chromosomes, while males have one X and one Y chromosome. The Y chromosome carries genes essential for male anatomical development. In female mammals, one X chromosome is inherited from the mother (the maternal X chromosome, or X_m) and the other is inherited from the father (the paternal X chromosome, or X_p). To maintain balanced gene expression between the sexes, one of the X chromosomes in each female cell is transcriptionally silenced early in embryonic development through a process called X chromosome inactivation.

This X chromosome inactivation ensures that females, like males, express only one functional copy of X-linked genes. It occurs by compacting one X chromosome into a tightly packed structure known as a Barr body, which suppresses gene transcription, while the other X chromosome remains active.¹ Typically, X chromosome inactivation is random, meaning each cell independently silences either the X_m or X_p, creating a mosaic pattern of X chromosome expression across tissues. This mosaicism is thought to provide a biological advantage by allowing gene expression from both parental X chromosomes.

However, X chromosome inactivation can sometimes become skewed, favoring the silencing of the same parental X chromosome in many or most cells. This skewing may arise due to differences in cell fitness or mutations that render one X chromosome more prone to inactivation. In such cases, the resulting imbalance can contribute to X-linked disorders, dysregulated cellular processes, or age-related cognitive decline.² In a new study, researchers at UCSF’s Weill Institute for Neurosciences investigated this phenomenon further. Specifically, they explored how skewing toward an active maternal X chromosome (X_m) affects cognition, biological aging, and organismal functions in females.³

Investigating the Maternal X Chromosome: A Landmark Study at UCSFA Landmark UCSF Study

In their recent Nature publication, Dr. Dena B. Dubal and colleagues used a mouse model to explore how skewed X inactivation toward the maternal X chromosome affects brain and body function over time. The researchers were able to isolate the effects of parent-of-origin gene expression by engineering female mice to express only the maternal X chromosome across all cells (X_m-only mice) and comparing them to control mice with normal random X inactivation (X_m+X_p).

The study first focused on identifying whether maternal X chromosome skew impacts cognitive function in female mice. At multiple stages of the lifespan—young adulthood, middle age, and old age—the mice underwent a series of behavioral tests, including the Morris water maze, open field test, elevated plus maze, and two-trial Y maze. Mice with maternal X skew demonstrated consistently lower performance in spatial memory and learning tasks compared to X_m+X_p controls, with deficits evident as early as young adulthood. These deficits became more pronounced with age, indicating that skewing toward the maternal X chromosome leads to age-related cognitive decline. In contrast, control mice with normal X mosaicism maintained significantly better cognitive performance across all timepoints.

Having established a clear link between maternal X skew and cognitive dysfunction, the researchers next investigated whether this genetic imbalance also contributes to accelerated biological aging, particularly in the brain. They focused on the hippocampus, a brain region crucial for memory formation and especially vulnerable to age-related degeneration. To assess epigenetic aging in each group of mice, the team analyzed DNA methylation patterns across 2,045 validated age-associated CpG loci in both the hippocampus and blood.

DNA was extracted from these tissues using Zymo Research’s Quick-DNA Miniprep Plus Kit, which provided high-yield, ultra-pure total DNA suitable for sensitive epigenetic applications in under 20 minutes. The purified DNA was then processed with the EZ DNA Methylation-Lightning Kit, a rapid bisulfite conversion kit that delivers >99.5% conversion efficiency in just 90 minutes, while minimizing DNA degradation and handling time—critical for sensitive downstream methylation analysis.

To quantify biological age, the team used Zymo’s DNAge^® Mouse Epigenetic Age Analysis service, which predicts biological age by assessing methylation patterns across over 2,000 CpG sites known to correlate with aging. The DNAge^® epigenetic clock leverages key differentially methylated regions (DMRs) to provide sensitive, quantitative estimates of tissue-specific epigenetic age. The analysis showed that while blood samples showed no significant differences in biological age between groups, the hippocampus of X_m-only mice exhibited higher epigenetic age compared to X_m+X_p controls, particularly in older animals. This provides strong evidence that maternal X skew selectively accelerates biological aging in the brain.

Interestingly, this effect was not observed in other systems. Cardiac, skeletal, and metabolic tissues from X_m-only mice did not show the same functional decline or increase in biological age. The authors attributed this tissue-specific effect to the high number of X-linked genes expressed in the brain, which may increase its sensitivity to skewed X chromosome inactivation.

Gene Silencing on the Maternal X ChromosomeEpigenetic Gene Silencing

To investigate the molecular mechanisms underlying accelerated brain aging in X_m-only mice, the UCSF team performed fluorescence-activated cell sorting (FACS) and RNA sequencing on genetically identical X_m and X_p neurons isolated from the hippocampus of female mice with random X chromosome inactivation. By using transgenic markers to distinguish neurons expressing either the maternal or paternal X chromosome, the researchers identified a set of nine genes—including Sash3, Tlr7, and Cysltr1—that were epigenetically silenced exclusively on the maternal X. These genes are involved in immune signaling and neuronal function, and their selective silencing pointed to a parent-of-origin imprinting effect. Notably, this silencing was not due to mutations in the DNA but instead caused by epigenetic regulation of the genes, highlighting the critical role of gene expression patterns in brain aging.

To test whether restoring expression of these genes could reverse age-related cognitive decline, the researchers used CRISPR activation (CRISPRa) to upregulate the silenced genes with the strongest expression differences between X_m and X_p neurons—Sash3, Tlr7, and Cysltr1. When mRNA expression of these genes was increased twofold specifically in the hippocampus of aged X_m-only mice, mitochondrial energy production improved in the neuronal population, and spatial learning and memory performance improved in the treated mice.

These findings indicated that restoring expression of key silenced genes on the maternal X chromosome, including Sash3, Tlr7, and Cysltr1, improves cognitive function in older female mice. This provided not only a compelling mechanistic insight but also a therapeutic proof-of-concept: epigenetic silencing driven by maternal X skew can impair cognition, and this impairment may be reversible through CRISPRa technology.

Implications for Human Health and AgingHealth & Aging Implications

This work suggests that female cognitive aging is influenced not just by mutations or environmental factors, but by epigenetic parent-of-origin modulation of gene expression at the chromosomal level. Specifically, skewed X chromosome inactivation favoring the maternal X may increase susceptibility to age-related cognitive decline and potentially heighten the risk for neurodegenerative diseases such as Alzheimer’s. Women with more balanced X mosaicism, by contrast, may be relatively protected from these conditions as they age.

The findings also underscore the importance of tools that can assess biological age at the tissue level. While most epigenetic aging clocks rely on accessible sample types like blood or saliva, the UCSF team showed that epigenetic aging in the brain—particularly the hippocampus—can diverge significantly from systemic measures. This highlights the value of tissue-specific aging analysis in uncovering early or localized signs of decline that may not be detectable through conventional systemic approaches.

Measure What Matters: DNAge^® and Epigenomics Tools from Zymo ResearchAdvanced Epigenomics Tools

This landmark study was made possible by advanced sample preparation and epigenetics technology from Zymo Research, delivering the performance, precision, sensitivity, and speed required to support a complex, tissue-specific investigation of brain aging. The research team needed high-quality DNA from fragile brain tissue, rapid and efficient bisulfite conversion for accurate methylation profiling, and a robust platform to translate that methylation data into biologically meaningful insights.

The DNAge^® Epigenetic Age Analysis service provided critical insight into subtle yet significant differences in tissue-specific biological aging—differences that would not have been captured by traditional chronological measures. Powered by reduced representation bisulfite sequencing (RRBS) and trained on a validated set of age-associated CpG sites, DNAge^® enables researchers to accurately quantify epigenetic age, a metric increasingly linked to disease risk, cognitive decline, and longevity.

These insights were supported by Zymo’s gold-standard methylation analysis tools, recognized for their high conversion efficiency, ease of use, and ultra-pure yields across even the most challenging sample types. Backed by decades of expertise in epigenetics and DNA/RNA purification, Zymo Research provides fully integrated workflows, from sample extraction through data interpretation. These technologies empower researchers in fields such as aging, neuroscience, cancer, and immunology to investigate complex biological processes at the molecular level.

Zymo Research delivers the reliable data and rapid turnaround required for today’s most demanding research projects. Contact us today to learn how our team can support your next epigenomics study, or explore our complete portfolio of DNA methylation and purification technologies.