Lymph node CD4+ T cell and thioglycollate-elicited peritoneal macrophage expression data from naïve young and old SJL/J and SJL-ChrY^B10.S male mice. Mus musculus

Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J background, we show that susceptibility to two diverse animal models of autoimmune disease, including experimental allergic encephalomyelitis (EAE) and experimental myocarditis, correlates with the natural variation in copy number of Sly and Rbmy multicopy ChrY genes. In the B6 background, ChrY possesses gene regulatory properties that impact both genome-wide gene expression and the presence of alternative splice variants in pathogenic CD4+ T cells. Using a ChrY consomic strain on the SJL background, we discovered a preference for ChrY-mediated gene regulation in macrophages, the immune cell subset underlying the EAE sexual dimorphism in SJL mice, rather than CD4+ T cells. Importantly, in both genetic backgrounds, an inverse correlation exists between the number of Sly and Rbmy ChrY gene copies and the number of significantly upregulated genes in immune cells, thereby supporting a link between copy number variation of Sly and Rbmy with the ChrY genetic element exerting regulatory properties. Moreover, in humans, an analysis of the CD4+ T cell transcriptome from male multiple sclerosis patients versus healthy controls provides further evidence for an evolutionarily conserved mechanism of gene regulation by ChrY. Thus, these data establish ChrY as a member of the regulatory genome in mammals due to its ability to regulate gene expression and alternative splicing in immune cells linked to disease. Overall design: Three biological replicates from young (≤4 weeks) and old (≥ 6 months) mice from each strain were pooled from 5 mice for each replicate. RNA was isolated from CD4+TCRB+ FAC sorted cells and from thioglycollate-elicited peritoneal macrophages.

阐明构成并调控调控基因组的DNA元件，对于复杂疾病的合理诊疗管理至关重要。本研究以C57BL/6J遗传背景下的Y染色体（ChrY）同源替换系小鼠为模型，发现两种不同自身免疫疾病动物模型——实验性变应性脑脊髓炎（EAE）与实验性心肌炎——的易感性，与Sly和Rbmy多拷贝ChrY基因的拷贝数自然变异显著相关。在B6遗传背景中，ChrY具备基因调控特性，可影响全基因组基因表达水平以及致病性CD4+ T细胞中的可变剪接变体丰度。我们采用SJL遗传背景下的ChrY同源替换系小鼠开展研究，发现ChrY介导的基因调控更偏好作用于巨噬细胞——这一免疫细胞亚群正是SJL小鼠EAE表型性别二态性的核心基础——而非CD4+ T细胞。值得注意的是，在两种遗传背景中，免疫细胞内Sly与Rbmy ChrY基因的拷贝数与显著上调基因的数量均呈负相关，这一结果支持了Sly与Rbmy的拷贝数变异与具备调控功能的ChrY遗传元件之间存在关联。此外，对男性多发性硬化患者与健康对照者的CD4+ T细胞转录组进行分析，为ChrY介导的基因调控存在进化保守机制提供了进一步证据。综上，本研究数据证实ChrY属于哺乳动物调控基因组的一员，因其可调控疾病相关免疫细胞内的基因表达与可变剪接。实验整体设计：每个品系的年轻（≤4周龄）与老年（≥6月龄）小鼠各设置3个生物学重复，每个重复由5只小鼠的样本混合制备。分别从经荧光激活细胞分选（FACS）得到的CD4+TCRB+细胞以及硫乙醇酸盐诱导的腹腔巨噬细胞中提取总RNA。