Evidence map›Paper›PMID 39351871›Full record

ArticleNucleic acids research2024

The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex.

Robert P Connacher, Richard T Roden, Kai-Lieh Huang, Amanda J Korte, Saathvika Yeruva, Noel Dittbenner, Anna J DesMarais, Chase A Weidmann, Thomas A Randall, Jason Williams and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. RNA-binding is the essential biological function of thebioRxiv : the preprint server for biology · 2026
    Article
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.

Robert P ConnacherDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Richard T RodenDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Kai-Lieh HuangDepartment of Biochemistry and Biophysics, University of Rochester Medical Center, 575 Elmwood Avenue, Rochester, NY 14642, USA.
Amanda J KorteDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Saathvika YeruvaDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Noel DittbennerDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Anna J DesMaraisDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.
Chase A WeidmannDepartment of Biological Chemistry, Center for RNA Biomedicine, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.ORCID 0000-0002-2941-0500
Thomas A RandallIntegrative Bioinformatics Support Group, National Institute of Environmental Health Sciences (NIEHS), 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.
Jason WilliamsEpigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.
Traci M Tanaka HallEpigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.ORCID 0000-0001-6166-3009
Eric J WagnerDepartment of Biochemistry and Biophysics, University of Rochester Medical Center, 575 Elmwood Avenue, Rochester, NY 14642, USA.
Aaron C GoldstrohmDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1214A 6-155 Jackson Hall, 321 Church Street S.E., Minneapolis, MN 55455, USA.ORCID 0000-0002-1867-8763

Funding

XenograftP30CA046592 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Eric R. Fearon · 1988 to 2026
$178.2M
Structural Studies Of Post-Transcriptional Gene RegulationZIAES050165 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI HALL, TRACI M · 2009 to 2025
$45.7M
Mass Spectrometry QuantitationZICES103005 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI WILLIAMS, JASON · 2018 to 2025
$9.2M
Request to Transfer R01GM105707-03 Novel regulatory mechanisms of Drosophila Pumilio and NanosR01GM105707 · NIGMS · UNIVERSITY OF MINNESOTA · PI GOLDSTROHM, AARON CHARLES · 2013 to 2022
$2.7M
mRNA regulatory functions of the Drosophila TRIM-NHL protein, BratR01GM145835 · NIGMS · UNIVERSITY OF MINNESOTA · PI GOLDSTROHM, AARON CHARLES · 2022 to 2025
$1.4M
Unraveling the MALAT1 lncRNA-protein interaction networks that drive lung cancer metastasisK22CA262349 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI WEIDMANN, CHASE A · 2021 to 2023
$486k
Edith Walters Jones and Robert Jones FellowshipIntramural NIH HHS ZIC ES103005Intramural Research Program of the National Institutes of HealthNCI NIH HHS K22 CA262349NCI NIH HHS P30 CA046592NIEHS NIH HHS ZIA-ES050165NIGMS NIH HHS R01 GM105707NIGMS NIH HHS R01 GM145835NIH HHS R01 GM145835University of Michigan Center for RNA BiomedicineUniversity of Rochester
6 · The paper itself

Abstract

The essential Drosophila RNA-binding protein Brain Tumor (Brat) represses specific genes to control embryogenesis and differentiation of stem cells. In the brain, Brat functions as a tumor suppressor that diminishes neural stem cell proliferation while promoting differentiation. Though important Brat-regulated target mRNAs have been identified in these contexts, the full impact of Brat on gene expression remains to be discovered. Here, we identify the network of Brat-regulated mRNAs by performing RNA sequencing (RNA-seq) following depletion of Brat from cultured cells. We identify 158 mRNAs, with high confidence, that are repressed by Brat. De novo motif analysis identified a functionally enriched RNA motif in the 3' untranslated regions (UTRs) of Brat-repressed mRNAs that matches the biochemically defined Brat binding site. Integrative data analysis revealed a high-confidence list of Brat-repressed and Brat-bound mRNAs containing 3'UTR Brat binding motifs. Our RNA-seq and reporter assays show that multiple 3'UTR motifs promote the strength of Brat repression, whereas motifs in the 5'UTR are not functional. Strikingly, we find that Brat regulates expression of glycolytic enzymes and the vacuolar ATPase complex, providing new insight into its role as a tumor suppressor and the coordination of metabolism and intracellular pH.

Indexed as

3' Untranslated RegionsDrosophila ProteinsGlycolysisRNA, MessengerVacuolar Proton-Translocating ATPasesAnimalsBinding SitesDNA-Binding ProteinsDrosophila melanogasterGene Expression RegulationNucleotide MotifsRNA-Binding Proteins3' Untranslated Regionsbrat protein, DrosophilaDNA-Binding ProteinsDrosophila ProteinsRNA-Binding ProteinsRNA, MessengerVacuolar Proton-Translocating ATPases

Identifiers

PMID39351871
PMCPMC11551770

What OpenQuestion holds

Textmetadata
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.