Evidence map›Paper›PMID 40057514›Full record

ArticleNature communications2025

Molecular model of TFIIH recruitment to the transcription-coupled repair machinery.

Tanmoy Paul, Chunli Yan, Jina Yu, Susan E Tsutakawa, John A Tainer, Dong Wang, Ivaylo Ivanov

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Review
  2. Topology Resetting During Transcription-Coupled Nucleotide Excision Repair.International journal of molecular sciences · 2026
    Review
  3. Review
  4. Article
  5. Review
  6. Review
  7. Mechanisms of DNA repair and mutagenesis induced by acetaldehyde, acrolein, aristolochic acids, and vinyl chloride.Journal of environmental science and health. Part C, Toxicology and carcinogenesis · 2025
    Review
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

7 authors.

Tanmoy PaulDepartment of Chemistry, Georgia State University, Atlanta, GA, USA.
Chunli YanDepartment of Chemistry, Georgia State University, Atlanta, GA, USA.ORCID http://orcid.org/0000-0001-5742-120X
Jina YuDepartment of Chemistry, Georgia State University, Atlanta, GA, USA.
Susan E TsutakawaMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-4918-4571
John A TainerMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-1659-2429
Dong WangDivision of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, CA, San Diego, USA.ORCID http://orcid.org/0000-0002-2829-1546
Ivaylo IvanovDepartment of Chemistry, Georgia State University, Atlanta, GA, USA. iivanov@gsu.edu.ORCID http://orcid.org/0000-0002-5306-1005

Funding

Transcription-Coupled & Replication-Associated Excision RepairP01CA092584 · NCI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI John A. Tainer · 2001 to 2026
$89.6M
Mesoscale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC)R35CA220430 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI John A. Tainer · 2018 to 2026
$7.6M
Molecular Mechanisms for DNA Damage Processing by Transcription MachineryR01GM102362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WANG, DONG · 2013 to 2025
$5.6M
Advanced Computational Modeling of Molecular Machines in Gene Regulation and DNA RepairR35GM139382 · NIGMS · GEORGIA STATE UNIVERSITY · PI IVANOV, IVAYLO NIKOLAEV · 2021 to 2025
$2.0M
Integrative Modeling of Biomolecular Machinery in Nucleotide Excision RepairR01ES032786 · NIEHS · GEORGIA STATE UNIVERSITY · PI Ivaylo Nikolaev Ivanov · 2022 to 2026
$1.7M
National Science Foundation (NSF) MCB 2027902NCI NIH HHS P01 CA092584NCI NIH HHS R35 CA220430NIEHS NIH HHS R01 ES032786NIGMS NIH HHS R01 GM102362NIGMS NIH HHS R35 GM139382U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM139382
6 · The paper itself

Abstract

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4

Indexed as

DNA RepairTranscription Factor TFIIHTranscription, GeneticCarrier ProteinsDNADNA-Binding ProteinsDNA DamageDNA HelicasesDNA Repair EnzymesExcision RepairHumansModels, MolecularPoly-ADP-Ribose Binding ProteinsProtein BindingRNA Polymerase IICarrier ProteinsDNADNA-Binding ProteinsDNA HelicasesDNA Repair EnzymesERCC6 protein, humanPoly-ADP-Ribose Binding ProteinsRNA Polymerase IITranscription Factor TFIIHUVSSA protein, human

Identifiers

PMID40057514
PMCPMC11890784

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.