In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates^1,2,3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT–ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT–ChA to CD34⁺ cells from patients with myeloproliferative neoplasms with JAK2^V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2^V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2^V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT–ChA will empower broad future investigations of the critical link between somatic mutations and epigenetic alterations across clonal populations in malignant and non-malignant contexts.

在体细胞组织分化中，染色质可及性的变化控制着细胞命运的启动和前体承诺^1,2,3。因此，体细胞突变可能会改变染色质可及性模式，因为它们破坏分化拓扑，导致异常的克隆生长。然而，由于突变型和野生型细胞的混合，确定体细胞突变对人类样本表观基因组的影响具有挑战性。在这里，为了描绘体细胞突变如何破坏人类克隆产物的表观遗传景观，我们开发了具有单细胞染色质可及性（GoT-ChA）的目标位点的基因分型。该高通量平台在单次检测中以单细胞分辨率将基因型与数千个细胞的染色质可及性联系起来。我们将 GoT–ChA 应用于来自具有JAK2 ^V617F突变造血功能的骨髓增殖性肿瘤患者的CD34 ⁺细胞。野生型和JAK2 ^V617F突变祖细胞之间的差异可及性分析揭示了突变造血前体细胞内细胞内在和细胞状态特异性的变化，包括造血干细胞中细胞内在的促炎症特征，以及独特的促纤维化炎症染色质景观在巨核细胞祖细胞中。线粒体基因组分析和细胞表面蛋白表达测量的整合允许通过插补将基因分型扩展到 DOGMA-seq，从而实现基因型的单细胞捕获、染色质可及性、RNA 表达和细胞表面蛋白表达。总的来说，我们发现JAK2 ^V617F突变导致以细胞内在和细胞类型特异性的方式进行表观遗传重连，影响炎症状态和分化轨迹。我们预计 GoT-ChA 将有助于未来对恶性和非恶性环境中克隆群体的体细胞突变和表观遗传改变之间的关键联系进行广泛的研究。