NASC-seq monitors RNA synthesis in single cells

• Published in: Nature communications Vol. 10; no. 1; pp. 3138 - 9
• Main Authors: Hendriks, Gert-Jan, Jung, Lisa A., Larsson, Anton J. M., Lidschreiber, Michael, Andersson Forsman, Oscar, Lidschreiber, Katja, Cramer, Patrick, Sandberg, Rickard
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.07.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/71; 38/91; 631/114/2397; 631/1647/2217/2018; 631/1647/514/1949; Alkylation; Cell activation; Differentiation (biology); Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation; Gene sequencing; Genes; Humanities and Social Sciences; Humans; Jurkat Cells; K562 Cells; Lymphocytes T; Monitoring; mRNA turnover; multidisciplinary; Perturbation; Ribonucleic acid; RNA; RNA - chemistry; Science; Science (multidisciplinary); Sequence Analysis, RNA - methods; Single-Cell Analysis; Synthesis; Temporal resolution; Transcription
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11028-9

Sequencing of newly synthesised RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesised and pre-existing RNA simultaneously in single cells. We validate the method on pre-labelled RNA, and by demonstrating that more newly synthesised RNA was detected for genes with known high mRNA turnover. Monitoring RNA synthesis during Jurkat T-cell activation with NASC-seq reveals both rapidly up- and down-regulated genes, and that induced genes are almost exclusively detected as newly transcribed. Moreover, the newly synthesised and pre-existing transcriptomes after T-cell activation are distinct, confirming that NASC-seq simultaneously measures gene expression corresponding to two time points in single cells. Altogether, NASC-seq enables precise temporal monitoring of RNA synthesis at single-cell resolution during homoeostasis, perturbation responses and cellular differentiation. Sequencing of newly synthesised RNA can reveal the transcriptional dynamics in a population of cells. Here the authors develop NASC-seq to bring this sensitivity and temporal resolution to single-cell analysis.