Evidence map›Paper›PMID 40741402›Full record

ArticleBio-protocol2025

Fast TV-PRO-seq: Accelerated and Streamlined Protocol for Timing RNA Polymerase Pausing.

Jie Zhang, Zhixian Liang, Mingxin Sun, Daniel Hebenstreit, Shaohui Zhang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bio-protocol, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Jie ZhangNational Engineering Research Center for Healthcare Devices & Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Materials, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China.
Zhixian LiangNational Engineering Research Center for Healthcare Devices & Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Materials, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China.
Mingxin SunThe College of Life Science and Technology, Jinan University, Guangzhou, China.
Daniel HebenstreitSchool of Life Sciences, Gibbet Hill Campus, The University of Warwick, CV4 7AL Coventry, UK.
Shaohui ZhangNational Engineering Research Center for Healthcare Devices & Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Materials, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Transcriptional pausing dynamically regulates spatiotemporal gene expression during cellular differentiation, development, and environmental adaptation. Precise measurement of pausing duration, a critical parameter in transcriptional control, has been challenging due to limitations in resolution and confounding factors. We introduce Fast TV-PRO-seq, an optimized protocol built on time-variant precision run-on sequencing (TV-PRO-seq), which enables genome-wide, single-base resolution mapping of RNA polymerase II pausing times. Unlike standard PRO-seq, Fast TV-PRO-seq employs sarkosyl-free biotin-NTP run-on with time gradients and integrates on-bead enzymatic reactions to streamline workflows. Key improvements include (1) reducing experimental time from 4 to 2 days, (2) reducing cell input requirements, and (3) improved process efficiency and simplified command-line operations through the use of bash scripts. Key features • Reduces experimental duration from 4 to 2 days via on-bead enzymatic reactions and streamlined workflows. • Enables single-nucleotide resolution pausing time mapping using time-variant biotin-NTP run-on with saturation kinetics. • Compatible with reduced cell input (10

Indexed as

Dynamic transcriptional regulationNascent transcriptionNext-generation sequencing (NGS)PRO-seqRNA polymerase II pausing durationRNA polymerase pausingSingle-base resolution

Identifiers

PMID40741402
PMCPMC12305362

What OpenQuestion holds

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Registered trials

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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.