Simultaneous Measurement of RNA Synthesis and Degradation Rates in Single Cells Unveils the Regulatory Mechanisms of Temporal RNA Dynamics
Abstract
Abstract The temporal dynamics of coordinated RNA transcription and degradation are heterogeneous among different cell types or states. However, current transcriptomic approaches are unable to simultaneously measure transcriptome‐wide RNA synthesis and degradation rates in single cells for resolving the RNA regulatory mechanisms during dynamic processes. Herein, we develop scDUAL‐seq, which integrates double nucleoside analogs pulse‐pulse labeling, chemical nucleoside conversion, and single‐cell RNA sequencing to record both RNA transcription and RNA degradation in heterogeneous cell populations. Compared to single nucleoside analog labeling‐based methods, scDUAL‐seq allows simultaneous recording of RNA transcription and degradation, leading to more accurate determination of RNA kinetic rates and RNA regulatory strategies. In a cortisol response model, scDUAL‐seq enables the discovery of key regulons driving strategy transitions and elucidation of the coordinated regulation of RNA synthesis and degradation rates that control distinct strategy transitions. scDUAL‐seq is expected to provide new insights into RNA regulatory mechanisms across diverse biological processes.
Article Details
Authors (5)
Siying Wang
State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine
Kun Yin
Jia Song
Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, College of Chemistry and Chemical Engineering
Shichao Lin
State Key Laboratory of Physical Chemistry of Solid Surfaces Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) State Key Laboratory of Vaccines for Infectious Diseases Xiang An Biomedicine Laboratory The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation Key Laboratory for Chemical Biology of Fujian Province Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
Chaoyong Yang
State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, School of Life Sciences, Faculty of Medicine and Life Sciences