Evidence map›Paper›PMID 27514584›Full record

ArticleBiochimica et biophysica acta2016

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.

A Rasim Barutcu, Deli Hong, Bryan R Lajoie, Rachel Patton McCord, Andre J van Wijnen, Jane B Lian, Janet L Stein, Job Dekker, Anthony N Imbalzano, Gary S Stein

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biochimica et biophysica acta, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.

0numbers the graph read from it
0cells of the map it votes in
43citing papers in PubMed
5.7field-weighted citation impact, top 3% of its field
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

43 citing papers in PubMed, 83 citations in OpenAlex.

  1. RUNX1-deficiency drives immune-active ERbioRxiv : the preprint server for biology · 2026
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  14. Nuclear Actin Dynamics in Gene Expression, DNA Repair, and Cancer.Results and problems in cell differentiation · 2022
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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

10 authors at 3 institutions in 1 country.

A Rasim BarutcuDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Deli HongDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
Bryan R LajoieProgram in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
Rachel Patton McCordProgram in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
Andre J van WijnenDepartment of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
Jane B LianDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
Janet L SteinDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
Job DekkerHoward Hughes Medical Institute, Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
Anthony N ImbalzanoDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA. Electronic address: anthony.imbalzano@umassmed.edu.
Gary S SteinDepartment of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address: gary.stein@uvm.edu.
University of Massachusetts Chan Medical School · USMayo Clinic · USUniversity of Vermont · US

Funding

SUBNUCLEAR TARGETING OF TRANSCRIPTION FACTORSP01CA082834 · NCI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI STEIN, GARY S. · 2001 to 2015
$18.4M
Structural Annotation of the Human GenomeR01HG003143 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI Job Dekker · 2003 to 2026
$15.4M
Howard Hughes Medical InstituteNCI NIH HHS P01 CA082834NHGRI NIH HHS R01 HG003143
6 · The paper itself

Abstract

RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organization. We characterized genome-wide RUNX1 localization and performed RNA-seq and Hi-C in RUNX1-depleted and control MCF-7 breast cancer cells. RNA-seq analysis showed that RUNX1 depletion led to up-regulation of genes associated with chromatin structure and down-regulation of genes related to extracellular matrix biology, as well as NEAT1 and MALAT1 lncRNAs. Our ChIP-Seq analysis supports a prominent role for RUNX1 in transcriptional activation. About 30% of all RUNX1 binding sites were intergenic, indicating diverse roles in promoter and enhancer regulation and suggesting additional functions for RUNX1. Hi-C analysis of RUNX1-depleted cells demonstrated that overall three-dimensional genome organization is largely intact, but indicated enhanced association of RUNX1 near Topologically Associating Domain (TAD) boundaries and alterations in long-range interactions. These results suggest an architectural role for RUNX1 in fine-tuning local interactions rather than in global organization. Our results provide novel insight into RUNX1-mediated perturbations of higher-order genome organization that are functionally linked with RUNX1-dependent compromised gene expression in breast cancer cells.

Indexed as

Gene Expression Regulation, NeoplasticBreast NeoplasmsChromatinChromatin ImmunoprecipitationExtracellular MatrixFemaleHumansMCF-7 CellsChromatinBreast cancerHi-CMCF-7RUNX1TADTopologically associating domain

Identifiers

PMID27514584
PMCPMC5071180
OpenAlexW2515073808

What OpenQuestion holds

Textmetadata
LicenceTDM
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.