Evidence map›Paper›PMID 40595470›Full record

ArticleNature communications2025

Structural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling.

Bradley P Clarke, Shengyan Gao, Menghan Mei, Dongqi Xie, Alexia E Angelos, Ashley Vazhavilla, Pate S Hill, Tolga Cagatay, Kimberly Batten, Jerry W Shay and 3 more

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 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Review
  2. Prion-Like Protein LENG8-Mediated Nucleation Drives Stress Granule Assembly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
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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

13 authors.

Bradley P ClarkeDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-9413-9905
Shengyan GaoDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Menghan MeiDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.ORCID http://orcid.org/0000-0001-7130-4659
Dongqi XieDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-7037-6335
Alexia E AngelosDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
Ashley VazhavillaDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Pate S HillDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
Tolga CagatayDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0003-0256-7636
Kimberly BattenDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Jerry W ShayDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-5052-0627
Yihu XieDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. yihu.xie@vanderbilt.edu.ORCID http://orcid.org/0000-0002-7729-3193
Beatriz M A FontouraDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Beatriz.Fontoura@UTSouthwestern.edu.ORCID http://orcid.org/0000-0001-8468-5315
Yi RenDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. yi.ren@vanderbilt.edu.ORCID http://orcid.org/0000-0003-4531-0910

Funding

Integrated Biological Systems Training in OncologyT32CA119925 · NCI · VANDERBILT UNIVERSITY · PI Vivian Gama, William Patrick Tansey · 2008 to 2026
$7.6M
Splicing and Nuclear Transport of Influenza Virus mRNAR01AI125524 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI COBB, MELANIE H., FONTOURA, BEATRIZ MA · 2016 to 2025
$5.6M
Virulence Factor at the Interface of Viral and Cellular mRNA Nuclear ExportR01AI154635 · NIAID · UT SOUTHWESTERN MEDICAL CENTER · PI Beatriz MA Fontoura · 2020 to 2026
$5.1M
Mechanisms and Regulation of Nuclear mRNA ExportR35GM133743 · NIGMS · VANDERBILT UNIVERSITY · PI Yi Ren · 2019 to 2026
$3.6M
mRNA Nuclear Export Machinery as Target of SARS-CoV-2 Nsp1 ProteinR01AI184975 · NIAID · VANDERBILT UNIVERSITY · PI Beatriz MA Fontoura, Adolfo Garcia-Sastre · 2024 to 2026
$2.5M
Thermo Scientific Glacios cryo-TEMS10OD030292 · OD · VANDERBILT UNIVERSITY · PI NAKAGAWA, TERUNAGA · 2021 to 2021
$2.0M
Molecular Basis for the TREX-2 mRNA Nuclear Export PathwayR01GM157478 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI FONTOURA, BEATRIZ MA · 2025 to 2025
$759k
NCI NIH HHS T32 CA119925NIAID NIH HHS R01 AI125524NIAID NIH HHS R01 AI154635NIAID NIH HHS R01 AI184975NIGMS NIH HHS R01 GM157478NIGMS NIH HHS R35 GM133743NIH HHS S10 OD030292U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) T32CA119925
6 · The paper itself

Abstract

Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a multifunctional regulator of nuclear mRNPs. How DDX39B mediates mRNP assembly and export in a controlled manner remains elusive. Here, we identify a novel complex TREX-2.1 localized in the nucleus that facilitates the release of DDX39B from the mRNP. TREX-2.1 is composed of three subunits, LENG8, PCID2, and DSS1, and shares the latter two subunits with the nuclear pore complex-associated TREX-2 complex. Cryo-EM structures of TREX-2.1/DDX39B and TREX-2/DDX39B identify a conserved trigger loop in the LENG8 and GANP subunit of the respective TREX-2.1 and TREX-2 complex that is critical for DDX39B regulation. RNA sequencing from LENG8 knockdown cells shows that LENG8 influences the nucleocytoplasmic ratio of a subset of mRNAs with high GC content. Together, our findings lead to a mechanistic understanding of the functional cycle of DDX39B and its regulation by TREX-2 and TREX-2.1 in mRNP processing.

Indexed as

DEAD-box RNA HelicasesRibonucleoproteinsActive Transport, Cell NucleusCell NucleusCryoelectron MicroscopyHEK293 CellsHeLa CellsHumansRNA, MessengerDDX39B protein, humanDEAD-box RNA Helicasesmessenger ribonucleoproteinRibonucleoproteinsRNA, Messenger

Identifiers

PMID40595470
PMCPMC12216326

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.