Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors

Abstract

Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from nascent RNA to mature RNA to degradation. To feed this kinetic analysis, simultaneous measurement of nascent RNA and mature RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry only captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based scRNA-seq method: snapTotal-seq. We benchmarked this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identified the critical regulatory hubs mediating the cell cycle dynamics. We also applied snapTotal-seq to profile the oncogene-induced senescence and identified the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of nascent RNA and mature RNA, we identified a significant portion of genes whose expression changes occurred in mature RNA but not to the same degree in nascent RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.