Single-cell nascent RNA sequencing unveils coordinated global transcription

• 成果类型: Article
• 署名作者: Mahat, Dig B.; Tippens, Nathaniel D.; Martin-Rufino, Jorge D.; Waterton, Sean K.; Fu, Jiayu; Blatt, Sarah E.; Sharp, Phillip A.
• 署名单位: Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT); Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Stanford University; Northwestern University
• 刊物名称: Nature
• ISSN/ISSBN: 0028-6033
• DOI: 10.1038/s41586-024-07517-7
• 发表日期: 2024-07-04
• 页码: 216-+
• 关键词: gene-expression; super-enhancers; genome; identification; polymerase; initiation; promoters; ELEMENTS; architecture; DYNAMICS

摘要

Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers(1,2). Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations(3). However, fundamental questions about the temporal regulation of transcription and enhancer-gene coordination remain unanswered, primarily because of the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq-a new single-cell nascent RNA sequencing assay that uses click chemistry-and unveil coordinated transcription throughout the genome. We demonstrate the episodic nature of transcription and the co-transcription of functionally related genes. scGRO-seq can estimate burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells and can leverage replication-dependent non-polyadenylated histone gene transcription to elucidate cell cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq enables the identification of networks of enhancers and genes. Our results suggest that the bursting of transcription at super-enhancers precedes bursting from associated genes. By imparting insights into the dynamic nature of global transcription and the origin and propagation of transcription signals, we demonstrate the ability of scGRO-seq to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.