Lyu Jun, Chen Chongyi
Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Int J Mol Sci. 2024 Nov 29;25(23):12845. doi: 10.3390/ijms252312845.
Transcriptome analysis in single cells, enabled by single-cell RNA sequencing, has become a prevalent approach in biomedical research, ranging from investigations of gene regulation to the characterization of tissue organization. Over the past decade, advances in single-cell RNA sequencing technology, including its underlying chemistry, have significantly enhanced its performance, marking notable improvements in methodology. A recent development in the field, which integrates RNA metabolic labeling with single-cell RNA sequencing, has enabled the profiling of temporal transcriptomes in individual cells, offering new insights into dynamic biological processes involving RNA kinetics and cell fate determination. In this review, we explore the chemical principles and design improvements that have enhanced single-molecule capture efficiency, improved RNA quantification accuracy, and increased cellular throughput in single-cell transcriptome analysis. We also illustrate the concept of RNA metabolic labeling for detecting newly synthesized transcripts and summarize recent advancements that enable single-cell temporal transcriptome analysis. Additionally, we examine data analysis strategies for the precise quantification of newly synthesized transcripts and highlight key applications of transcriptome and temporal transcriptome analyses in single cells.
通过单细胞RNA测序实现的单细胞转录组分析，已成为生物医学研究中的一种普遍方法，涵盖从基因调控研究到组织组织特征描述等多个领域。在过去十年中，单细胞RNA测序技术的进步，包括其基础化学原理，显著提升了其性能，在方法学上取得了显著改进。该领域的一项最新进展，即将RNA代谢标记与单细胞RNA测序相结合，能够对单个细胞中的时间转录组进行分析，为涉及RNA动力学和细胞命运决定的动态生物学过程提供了新的见解。在这篇综述中，我们探讨了提高单分子捕获效率、改善RNA定量准确性以及增加单细胞转录组分析中细胞通量的化学原理和设计改进。我们还阐述了用于检测新合成转录本的RNA代谢标记概念，并总结了实现单细胞时间转录组分析的最新进展。此外，我们研究了用于精确量化新合成转录本的数据分析策略，并强调了转录组和时间转录组分析在单细胞中的关键应用。
