Evidence map›Paper›PMID 40117000›Full record

ArticleFunctional & integrative genomics2025

DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility.

Simone D Hall, Khoa Tran, Jonathan Zhu, Tong Su, Colleen A McHugh

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Functional & integrative genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Trial
  2. Review
  3. Review
  4. Review
  5. 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

5 authors.

Simone D HallDepartment of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA.
Khoa TranDepartment of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA.
Jonathan ZhuDepartment of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA.
Tong SuDepartment of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA.
Colleen A McHughDepartment of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA. c1mchugh@ucsd.edu.

Funding

Contemporary Approaches to Cancer Cell Signaling and CommunicationT32CA009523 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DONOGHUE, DANIEL J, YANG, JING · 1985 to 2025
$12.1M
MOLECULAR BIOPHYSICS TRAINING PROGRAMT32GM008326 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KOMIVES, ELIZABETH A. · 1989 to 2020
$7.5M
Mechanisms of large non-coding RNA regulation of gene expressionR00GM120494 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MCHUGH, COLLEEN ADARE · 2018 to 2020
$747k
NCI NIH HHS T32 CA009523NIGMS NIH HHS R00 GM120494NIGMS NIH HHS T32 GM008326University of California Cancer Research Coordinating Committee C21CR2119
6 · The paper itself

Abstract

Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (Dppa2 upstream binding RNA, also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltransferases. High expression levels of this ncRNA are predictive of poor patient outcome in colon adenocarcinoma, suggesting that DUBR may be involved in controlling cancer growth. To elucidate its function, we used RAP-MS and RNA immunoprecipitation techniques which revealed its interaction with epigenetic maintenance proteins in the human colon cancer cell line HCT116. Further, ATAC-seq and RNA-seq were used to address its function in regulating the epigenome and transcriptome of HCT116 cells. Here we report that DUBR is a regulator of human colon cancer cell line HCT116 survival. Additionally, we find that the ncRNA DUBR regulates AP-1 transcription factor binding site accessibility at enhancers of genes involved in differentiation and morphogenesis through interactions with epigenetic proteins such as NuRD complex members HDAC1 and CHD4.

Indexed as

Colonic NeoplasmsEnhancer Elements, GeneticGene Expression Regulation, NeoplasticRNA, Long NoncodingTranscription Factor AP-1Binding SitesEpigenesis, GeneticHCT116 CellsHistone Deacetylase 1HumansHDAC1 protein, humanHistone Deacetylase 1RNA, Long NoncodingTranscription Factor AP-1AP-1DUBRHCT116NuRD complexRAP-MS

Identifiers

PMID40117000
PMCPMC11928367

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.