Evidence map›Paper›PMID 40570372›Full record

ArticleCell reports2025

Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3' ends.

Olivia Luyties, Lynn Sanford, Jessica Rodino, Michael Nagel, Taylor Jones, Jenna K Rimel, Christopher C Ebmeier, Megan Palacio, Grace S Shelby, Kira Cozzolino and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2025. 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. Article
  2. Review
  3. Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Olivia LuytiesDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Lynn SanfordDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
Jessica RodinoDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Michael NagelDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Taylor JonesDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Jenna K RimelDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Christopher C EbmeierDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Megan PalacioDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Grace S ShelbyDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Kira CozzolinoDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Finn BrennanDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Axel HartzogDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Mirzam B SaucedoDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Lotte P WattsDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
Sabrina SpencerDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
Jennifer F KugelDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Robin D DowellDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
Dylan J TaatjesDepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA. Electronic address: taatjes@colorado.edu.

Funding

Supplemental request for MAX-TL Ultracentrifuge and rotorR35GM139550 · NIGMS · UNIVERSITY OF COLORADO · PI Dylan J Taatjes · 2021 to 2026
$3.8M
Unraveling the biological roles of specific miRNAs, from experimental target identification through functional characterizationR01GM148613 · NIGMS · UNIVERSITY OF COLORADO · PI Jennifer F. Kugel · 2023 to 2026
$1.3M
Q Exactive HF Nanoflow LC Mass Spectrometry SystemS10OD025267 · OD · UNIVERSITY OF COLORADO · PI AHN, NATALIE G. · 2018 to 2018
$600k
Acquisition of multi-mode, high-resolution, high-sensitivity imaging platformS10OD034218 · OD · UNIVERSITY OF COLORADO · PI ERBSE, ANNETTE H · 2023 to 2023
$153k
How do CDK7 and CDK9 regulate Pol II initiation and pausing?F31CA254478 · NCI · UNIVERSITY OF COLORADO · PI LUYTIES, OLIVIA CARON · 2020 to 2022
$115k
NCI NIH HHS F31 CA254478NIGMS NIH HHS R01 GM148613NIGMS NIH HHS R35 GM139550NIH HHS S10 OD025267NIH HHS S10 OD034218
6 · The paper itself

Abstract

CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely understood mechanisms. Because contaminating kinases prevent reliable CDK7 analysis with nuclear extracts, we reconstitute RNAPII transcription with purified factors. We show that CDK7 inhibition slows and/or pauses RNAPII promoter-proximal transcription and suppresses re-initiation, and these effects are Mediator and TFIID dependent. Similarly in human cells, CDK7 inhibition reduces transcriptional output by suppressing RNAPII initiation and/or re-initiation. Moreover, widespread 3' end readthrough transcription occurs in CDK7-inhibited cells; mechanistically, this results from rapid nuclear depletion of RNAPII elongation and termination factors (e.g., DSIF, Integrator, NELF, SPT6, PPP1R10/PNUTS, and SCAF8), including high-confidence CDK7 kinase targets. Collectively, these results define how CDK7 governs RNAPII function at gene 5' ends and 3' ends and reveal that nuclear abundance of elongation and termination factors is kinase dependent. Because 3'-readthrough transcription is commonly induced during stress, our results further suggest that regulated suppression of CDK7 activity enables this transcriptional response.

Indexed as

Cyclin-Dependent KinasesRNA Polymerase IICyclin-Dependent Kinase-Activating KinaseHumansMultiomicsPromoter Regions, GeneticTranscription, GeneticCDK7 protein, humanCyclin-Dependent Kinase-Activating KinaseCyclin-Dependent KinasesRNA Polymerase II3’-readthrough transcriptionCDK7CP: Molecular biologyin vitro transcriptionMediatorpromoter escapepromoter-proximal pausingPRO-seqproteomicsre-initiationRNA polymerase IITFIID

Identifiers

PMID40570372
PMCPMC12329788

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.