Expression of Y-Chromosome-Encoded Specific Genes in Mouse and Human Brain Neurons and Their Potential Impact on Sex Differences

Traditional paradigms hold that Y-chromosome-encoded genes are predominantly expressed in the testes, where they regulate male sexual development and fertility. However, whether these genes are expressed in brain tissue and their functional significance therein have long been overlooked. In this study, we employed C4 single-cell sequencing technology and detected the expression of 11 Y-chromosome-encoded genes in the mouse brain, including DDX3Y, USP9Y, KDM5D, Eif2s3y, Uty, II3ra, II9r, Spry3, Asmt, Zfy1, and Zfy2. The expression of KDM5D, Eif2s3y, and Uty was validated by RNA in situ hybridization (RNA-ISH), and the protein expression of DDX3Y and USP9Y was confirmed by immunofluorescence staining. These genes were found to be predominantly expressed in neurons, with lower expression levels observed in glial cells. Comparative analysis of expression changes between 3-month-old and 14-month-old mouse brains revealed that Uty expression was upregulated in neurons of aged mice and became clearly detectable in glial cells; DDX3Y, KDM5D, and Eif2s3y also showed increased expression in neurons; whereas Usp9y expression remained low but detectable. Finally, DDX3Y expression was examined in human brain tissue and was found to be predominantly distributed in neurons of the cerebral gray matter, with lower expression in the white matter. Collectively, this study provides the first systematic evidence of in situ expression of Y-chromosome-encoded proteins in mammalian brain neurons and glial cells, offering a direct molecular basis for understanding male–female brain differences independent of sex hormones, and provides new insights into sex bias in neurological disorders.