Competition shapes the landscape of X-linked genetic diversity [scRNA-seq]

Human populations harbour sequence variants even within essential genes. As a result of random X chromosome inactivation (XCI) and epigenetically stable XCI propagation, X-linked variation gives rise to genetically diverse clones that co-exist within XX individuals. Whether interactions between such clones shape the deployment of X-linked diversity remains to be explored. To address this question, we focus on benign coding variation in the X-linked STAG2 gene. Mouse models reveal that clones expressing Stag2 variants contribute to tissues such as skin and brain at the expected frequencies, but show reduced contributions to the haematopoietic stem and progenitor cell pool, and severely defective lymphoid specification. Unexpectedly, the absence of Xvariant clones from the lymphoid compartment is due not to cell-intrinsic defects, but requires competitive interactions with Xwt clones: in the absence of Xwt, Xvariant cells generate normal numbers of functional lymphocytes. X-linked competition has hallmarks of non-cell-autonomous 'cell competition', known to operate in a range of biological processes including embryonic development, aging, and cancer. These findings show that interactions between genetically diverse clones that may operate in any XX individual can shape the contribution of X-linked diversity to specific cell types and tissues. Bone marrow cells isolated from heterozygous Stag2-WT x Stag2-R370Q Atrx-Luc/bGal female mice were depleted of lineage markers. FITC+ (Stag2-R370Q) and FITC- (Stag2-WT) cells were sorted and analyzed by scRNAseq.即便在必需基因中，人类群体也存在序列变异。由于随机X染色体失活（X chromosome inactivation, XCI）以及表观遗传上稳定的XCI传递过程，X连锁变异会产生遗传多样性的克隆，这些克隆共存于XX型个体体内。此类克隆间的相互作用是否会影响X连锁多样性的分配模式，目前仍有待探究。 为解答这一问题，我们聚焦于X连锁STAG2基因上的良性编码变异。小鼠模型实验显示，表达Stag2变异体的克隆可按预期频率定植于皮肤、大脑等组织，但在造血干细胞及祖细胞池中的占比有所降低，且淋巴谱系特化存在严重缺陷。令人意外的是，淋巴区室中缺失X变异型克隆并非源于细胞内在缺陷，而是需要与X野生型（X wild type, Xwt）克隆发生竞争性相互作用：在缺乏Xwt克隆的情况下，X变异型细胞可产生数量正常的功能性淋巴细胞。这种X连锁竞争具有非细胞自主性“细胞竞争”的特征，该过程已被证实可在胚胎发育、衰老及癌症等多种生物学过程中发挥作用。 上述研究结果表明，任何XX型个体体内都可能存在的遗传多样性克隆间的相互作用，能够决定X连锁多样性在特定细胞类型与组织中的占比情况。从杂合子Stag2-WT × Stag2-R370Q Atrx-Luc/bGal雌性小鼠体内分离的骨髓细胞，经谱系标记物清除处理后，将FITC阳性（Stag2-R370Q）与FITC阴性（Stag2-WT）细胞分选出来，通过单细胞RNA测序（single-cell RNA sequencing, scRNAseq）进行分析。