During multicellular development, spatial position and lineage history play powerful roles in controlling cell fate decisions. Using a serine integrase–based recording system, we engineered cells to record lineage information in a format that can be read out in situ. The system, termed integrase-editable memory by engineered mutagenesis with optical in situ readout (intMEMOIR), allowed in situ reconstruction of lineage relationships in cultured mouse cells and flies. intMEMOIR uses an array of independent three-state genetic memory elements that can recombine stochastically and irreversibly, allowing up to 59,049 distinct digital states. It reconstructed lineage trees in stem cells and enabled simultaneous analysis of single-cell clonal history, spatial position, and gene expression in Drosophila brain sections. These results establish a foundation for microscopy-readable lineage recording and analysis in diverse systems.

在多细胞发育过程中，空间位置和谱系历史在控制细胞命运决策中发挥着重要作用。使用基于丝氨酸整合酶的记录系统，我们设计了细胞以可原位读出的格式记录谱系信息。该系统被称为整合酶可编辑记忆，通过光学原位读出工程诱变（intMEMOIR），允许原位重建培养的小鼠细胞和果蝇的谱系关系。 intMEMOIR 使用一系列独立的三态遗传记忆元件，可以随机且不可逆地重新组合，最多允许 59,049 个不同的数字状态。它重建了干细胞中的谱系树，并能够同时分析果蝇大脑切片中的单细胞克隆历史、空间位置和基因表达。这些结果为不同系统中显微镜可读的谱系记录和分析奠定了基础。