Current approaches to single-cell RNA sequencing (RNA-seq) provide only limited information about the dynamics of gene expression. Here we present RNA timestamps, a method for inferring the age of individual RNAs in RNA-seq data by exploiting RNA editing. To introduce timestamps, we tag RNA with a reporter motif consisting of multiple MS2 binding sites that recruit the adenosine deaminase ADAR2 fused to an MS2 capsid protein. ADAR2 binding to tagged RNA causes A-to-I edits to accumulate over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we can determine when the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events. Finally, we apply the method to cluster single cells according to the timing of past transcriptional activity. RNA timestamps will allow the incorporation of temporal information into RNA-seq workflows.

当前的单细胞RNA测序（RNA-seq）方法仅提供有关基因表达动力学的有限信息。在这里，我们介绍了RNA时间戳，一种通过利用RNA编辑来推断RNA序列数据中单个RNA年龄的方法。为了引入时间戳，我们用带有多个MS2结合位点的报告子基元标记RNA，该结合位点募集与MS2衣壳蛋白融合的腺苷脱氨酶ADAR2。ADAR2与标记RNA的结合会导致A-to-I编辑随着时间的推移而积累，从而可以小时刻度精度推断出RNA的年龄。通过结合对同一启动子驱动的多个带有时间戳记的RNA的观察，我们可以确定启动子何时处于活动状态。我们证明该系统可以推断多个过去的转录事件的存在和定时。最后，我们根据过去转录活动的时间，将该方法应用于单个细胞的聚类。RNA时间戳将允许将时间信息整合到RNA序列工作流程中。