scDUAL-seq Simultaneously Measures RNA Synthesis and Degradation Rates in Single Cells

The interplay between RNA transcription and degradation tightly regulates the dynamic changes of RNA abundance. To unveil the underlying regulatory mechanism of RNA in shaping gene expression patterns, it is essential yet challenging to profile the coordinated regulation of RNA synthesis and degradation rates at the single-cell level during dynamic programs such as cell differentiation and cell state transition. Herein, we propose scDUAL-seq, a double metabolic RNA labeling-based single-cell RNA sequencing method to simultaneously measure RNA synthesis and degradation rates in thousands of single cells during dynamic processes. In a cortisol response model of colorectal cancer cells, scDUAL-seq identifies the RNA regulatory strategies for 5,930 genes, discovers key regulons driving the strategy transitions, and disentangles the interplay between RNA synthesis and degradation that control distinct strategy transitions during cortisol response. We anticipate that scDUAL-seq will be broadly applied to record RNA kinetic rates and the underlying regulatory mechanism in diverse dynamic processes. Overall design: mRNA profiles of dual metabolically labeled HCT116 and HEK293T in bulk assays and single-cell levels.