HisTrac-seq enables simultaneous profiling of past and present whole-genome chromatin states in single cells by enzymatically depositing stable m6A bookmarks that persist for months in vivo, revealing that 20-30% of differentiating neurons undergo large-scale disruptive identity transitions driven by premature activation of developmental programs through enhancer activation and bivalent chromatin resolution.

Advances in single-cell sequencing have deepened our understanding of cellular identities. However, because they inherently capture only static snapshots, after which no further observations are possible, we cannot compare past and present profiles within the same cell. Thus, multi-time-point whole-genome profiling at single-cell resolution has been a long-standing goal. Here, we introduce the History Tracing-sequencing (HisTrac-seq) platform, which enzymatically labels genomic DNA adenine to “bookmark” gene regulatory statuses. This first enabled the profiling of transcriptomic and epigenetic states in the mouse brain over a period of two months. Furthermore, extending HisTrac-seq to single-cell multi-omics sequencing, we demonstrated the simultaneous mapping of past and present profiles of the same single cells. Analyzing over 93,000 cells, we discovered unexpected, drastic cell identity transitions on a large scale (“identity jumps”). This phenomenon was previously unobservable with current technologies and revealed a hidden layer of developmental plasticity. HisTrac-seq offers a powerful approach to “temporal multi-omics” for disentangling dynamic biological processes involved in development, plasticity, aging, and disease progression.