SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle

We combined RNA metabolic labeling and alkylation with droplet-based sequencing to detect newly synthesized mRNAs in single cells. With the classification of labeled and unlabeled precursor and mature mRNAs, we modeled and analyzed the time-dependent RNA kinetic rates associated with the cell cycle. We found both transcription and degradation rates are highly dynamic over the cell cycle and different kinetic regulation types were observed for cycling genes. Overall design: Single cell and bulk RNA-seq of 4sU labeled, fixed and alkylated transcripts in HEK293 cells.

本研究将RNA代谢标记（RNA metabolic labeling）与烷基化（alkylation）技术结合，并搭配基于液滴的测序（droplet-based sequencing），以在单细胞层面检测新合成的信使RNA（messenger RNA, mRNA）。通过对标记及未标记的前体、成熟mRNA进行分类，本研究对与细胞周期相关的时间依赖性RNA动力学速率开展建模与分析。研究发现，转录速率与降解速率在细胞周期中均呈现高度动态变化，且周期基因存在多种不同的动力学调控模式。整体实验设计：对HEK293细胞中经4sU（4-硫尿苷）标记、固定及烷基化的转录本开展单细胞RNA测序与批量RNA测序。