Single-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Previous studies showed age-associated DNA methylation (DNAm) changes in specific genomic regions, termed clock-like differential methylation loci (ClockDML). Age-associated DNAm could either result from or result in chromatin accessibility changes at ClockDML. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. In this study, we developed a method, called EpiTrace, that counts the fraction of opened clock-like loci from scATAC-seq data to determine cell age and perform lineage tracing in various cell lineages and animal species. It shows concordance with known developmental hierarchies, correlates well with DNAm-based clocks and is complementary with mutation-based lineage tracing, RNA velocity and stemness predictions. Applying EpiTrace to scATAC-seq data reveals biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification.

单细胞染色质可及性测序 (scATAC-seq) 通过表型相似性重建发育轨迹。然而，推断确切的发展轨迹具有挑战性。先前的研究表明特定基因组区域中与年龄相关的 DNA 甲基化 (DNAm) 发生变化，称为类时钟差异甲基化位点 (ClockDML)。与年龄相关的 DNAm 可能是由 ClockDML 的染色质可及性变化引起或导致的。当细胞进行有丝分裂时，时钟样基因座上染色质可及性的异质性降低，从而提供有丝分裂年龄的测量。在这项研究中，我们开发了一种名为 EpiTrace 的方法，该方法可以计算 scATAC-seq 数据中开放的时钟样基因座的分数，以确定细胞年龄并在各种细胞谱系和动物物种中进行谱系追踪。它与已知的发育层次结构一致，与基于 DNAm 的时钟密切相关，并与基于突变的谱系追踪、RNA 速度和干性预测互补。将 EpiTrace 应用于 scATAC-seq 数据揭示了具有临床相关意义的生物学见解，范围从造血、器官发育、肿瘤生物学和免疫到皮质回旋。