Evidence map›Paper›PMID 37328900›Full record

ArticleGenome biology2023

Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.

David M Edwards, Philip Davies, Daniel Hebenstreit

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

David M EdwardsSchool of Life Sciences, University of Warwick, Coventry, UK. david.m.edwards@warwick.ac.uk.
Philip DaviesSchool of Life Sciences, University of Warwick, Coventry, UK.
Daniel HebenstreitSchool of Life Sciences, University of Warwick, Coventry, UK. d.hebenstreit@warwick.ac.uk.ORCID 0000-0003-0144-6728

Funding

Biotechnology and Biological Sciences Research Council BB/M01116X/1
6 · The paper itself

Abstract

Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical model and Bayesian inference implementation to facilitate genome-wide joint parameter estimation and confidence quantification (R package: burstMCMC). We demonstrate that, unlike conventional scRNA-seq, 4sU scRNA-seq resolves temporal parameters and furthermore boosts inference of dimensionless parameters via a synergy between single-cell resolution and 4sU labelling. We apply our method to published 4sU scRNA-seq data and linked with ChIP-seq data, we uncover previously obscured associations between different parameters and histone modifications.

Indexed as

Chromatin Immunoprecipitation SequencingThiouridineBayes TheoremRNA-SeqStaining and LabelingThiouridine4sUBurstingDynamicsGenome-wideHistone modificationInferenceSingle-cellTime-resolvedTranscription

Identifiers

PMID37328900
PMCPMC10276402

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.