Letter reSeArCH
regulation of promoter activity on the timescale of hours by temporar-
ily rendering gene promoters non-permissive. Finally, B-scores were
highly correlated with the observed heterogeneity in the transcriptomes
of individual cells (Fig. 4e). Gene promoter-specific features thus rep-
resent a major contributor to intercellular heterogeneity.
Metabolic labelling using 4sU is applicable to all major model
organisms including vertebrates, insects, plants and yeast. The purine
analogue 6-thioguanine (6sG) now also enables G-to-A conversions
by oxidative-nucleophilic-aromatic substitution (TimeLapse-seq
chemistry)^24. Short, consecutive pulses of 4sU and 6sG followed by
thiol-(SH)-mediated nucleoside conversions may enable two inde-
pendent recordings of transcriptional activity in single cells. Finally,
scSLAM-seq combined with CRISPR-based perturbations will greatly
improve the sensitivity of the respective approaches to decipher the
molecular mechanisms with major implications for developmental
biology, infection and cancer.
Reporting summary
Further information on research design is available in the Nature Research
Reporting Summary linked to this paper.
Data availability
The sequencing data and gene tables are available from the Gene Expression
Omnibus (GEO) with accession number GSE115612. The script files are
available at zenodo (doi: 10.5281/zenodo.1299119). GRAND-SLAM is available
for non-commercial use at http://software.erhard-lab.de.
Online content
Any methods, additional references, Nature Research reporting summaries, source
data, extended data, supplementary information, acknowledgements, peer review
information; details of author contributions and competing interests are available
at https://doi.org/10.1038/s41586-019-1369-y.
Received: 7 August 2018; Accepted: 10 June 2019;
Published online 10 July 2019.
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