scSLAM-seq reveals core features of transcription dynamics in single cells.
Nature, 2019/07;571(7765):419-423.
Erhard F[1], Baptista MAP[2], Krammer T[3], Hennig T[2], Lange M[4, 5], Arampatzi P[6], Jürges CS[2], Theis FJ[4, 5], Saliba AE[7], Dölken L[8, 9]
Affiliations
PMID: 31292545DOI: 10.1038/s41586-019-1369-y
Impact factor: 69.504
Abstract
Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease1. However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling2, biochemical nucleoside conversion3 and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.
MeSH terms
Alkylation; Animals; Cell Cycle; Cytomegalovirus; DNA Methylation; Fibroblasts; Gene Expression Regulation; Kinetics; Mice; Promoter Regions, Genetic; RNA; Sequence Analysis, RNA; Single-Cell Analysis; Sulfhydryl Compounds; Transcription, Genetic
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