Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription.

Autor:	Mahat DB; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139., Tippens ND; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139., Martin-Rufino JD; Broad Institute of MIT and Harvard, Cambridge, MA 02142., Waterton SK; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.; Current address: Department of Biology, Stanford University, Stanford, CA 94305., Fu J; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.; Current address: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208., Blatt SE; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.; Current address: Exact Sciences Corporation, Madison, WI 53719., Sharp PA; Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.; Lead Contact.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2023 Sep 19. Date of Electronic Publication: 2023 Sep 19.
DOI:	10.1101/2023.09.15.558015
Abstrakt:	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 1-5 . Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations 6-9 . However, fundamental questions in the temporal regulation of transcription and enhancer-gene synchrony remain unanswered primarily due to the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq - a novel single-cell nascent RNA sequencing assay using click-chemistry - and unveil the coordinated transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription, and estimates burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells. It reveals the co-transcription of functionally related genes and leverages the replication-dependent non-polyadenylated histone genes transcription to elucidate cell-cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq identifies networks of enhancers and genes and indicates that the bursting of transcription at super-enhancers precedes the burst from associated genes. By imparting insights into the dynamic nature of transcription and the origin and propagation of transcription signals, scGRO-seq demonstrates its unique ability to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression. Competing Interests: Competing interests US patent number US-11519027-B2 on ‘SINGLE-CELL RNA SEQUENCING USING CLICK-CHEMISTRY” was granted on December 6, 2022, to the Massachusetts Institute of Technology, Cambridge, MA (US), on which P.A.S. and D.B.M. are inventors. The authors declare no other competing interests.
Databáze:	MEDLINE
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