Evidence map›Paper›PMID 41331087›Full record

ArticleNature cell biology2026

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.

Yeqiao Zhou, Atishay Jay, Noah Burget, Tobias Friedrich, Sora Yoon, Jessica Alsing, Guy Nir, Rudolf Grosschedl, Golnaz Vahedi, Robert B Faryabi

Abstract read
In one paragraph

Article in Nature cell biology, 2026. 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. Article
  2. Article
  3. Review
  4. Article
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Yeqiao Zhou *Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-9422-6902
Atishay Jay *Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-3739-6726
Noah BurgetDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Tobias FriedrichDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-4014-8678
Sora YoonDepartment of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Jessica AlsingDepartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA.ORCID http://orcid.org/0000-0002-8558-6471
Guy NirDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.ORCID http://orcid.org/0000-0001-9268-6596
Rudolf GrosschedlMax Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.ORCID http://orcid.org/0000-0002-0058-1250
Golnaz VahediInstitute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0002-2249-8247
Robert B FaryabiDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA. faryabi@pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0002-7931-2175

Funding

Human Pancreas Analysis Program for Type 1 Diabetes - HPAP-T1DU01DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI MARK A. ATKINSON, KLAUS H KAESTNER · 2021 to 2026
$46.8M
The Human Pancreas Analysis Program for Type 2 DiabetesU01DK123594 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI Robert Babak Faryabi, KLAUS H KAESTNER · 2019 to 2026
$25.0M
3-Dimensional genomic architecture in innate lymphoid cells and allergic inflammationR01AI168240 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENAO-MEJIA, JORGE, VAHEDI, GOLNAZ · 2022 to 2025
$3.2M
3D genome organization of the Ets1-Fli1 locus controls allergic responsesR01AI168136 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Jorge Henao-Mejia, Golnaz Vahedi · 2023 to 2026
$3.1M
Critical role of TCF-1 on the epigenetic identity of memory T cellsR01HL145754 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI VAHEDI, GOLNAZ · 2019 to 2023
$2.3M
Notch-driven Epigenetic Program of MYC and CCND1 in Triple-Negative Breast CancerR01CA230800 · NCI · UNIVERSITY OF PENNSYLVANIA · PI FARYABI, ROBERT BABAK · 2020 to 2025
$2.1M
Epigenetic Mechanisms Underpinning Mantle Cell Lymphoma Sensitivity and Resistance to Notch InhibitorsR01CA248041 · NCI · UNIVERSITY OF PENNSYLVANIA · PI Robert Babak Faryabi · 2022 to 2026
$2.1M
Dissecting transcriptomics and epigenomic signatures of immune cells in type 1 diabetesU01DK127768 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI VAHEDI, GOLNAZ, WHERRY, E. JOHN · 2020 to 2023
$2.0M
NCI NIH HHS R01 CA230800NCI NIH HHS R01 CA248041NHLBI NIH HHS R01 HL145754NIAID NIH HHS R01 AI168136NIAID NIH HHS R01 AI168240NIDDK NIH HHS U01 DK112217NIDDK NIH HHS U01 DK123594NIDDK NIH HHS U01 DK127768U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01-CA-230800U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01-CA-248041U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) R01-HL145754U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) U01-DK-112217U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) U01-DK-123594U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) U01-DK127768
6 · The paper itself

Abstract

Multiple enhancers, often separated by vast genomic distances, regulate key genes. However, how the folding of individual chromatin fibres enables cell-type-restricted multi-enhancer regulation remains unclear. Here, using acute protein degradation and time-resolved chromatin conformation capture in mantle cell lymphoma, we found that the B cell-lineage-determining factor EBF1 organizes multiple enhancers around sparsely distributed genes essential for B cell identity and oncogenesis. Time-resolved sub-diffraction optical tracing of more than 100,000 chromatin fibres further revealed diverse topological conformations that facilitate multi-enhancer interactions. Mechanistically, we discovered that enhancer positioning at local topological centres is required for promoter engagement, with EBF1 acting as a permeable barrier to loop-extruding cohesin at enhancers. Extending these findings to T cell leukaemia, we show that lineage-determining transcription factors such as EBF1 and TCF1 radially position enhancers within gene loci to enable multi-enhancer regulation of key oncogenes at the single-allele level.

Indexed as

Cell Cycle ProteinsCell LineageChromosomal Proteins, Non-HistoneEnhancer Elements, GeneticLymphoma, Mantle-CellOncogenesTrans-ActivatorsAnimalsB-LymphocytesCell Line, TumorChromatinCohesinsGene Expression Regulation, NeoplasticHumansPromoter Regions, GeneticCell Cycle ProteinsChromatinChromosomal Proteins, Non-HistoneCohesinsEBF1 protein, humanTrans-Activators

Identifiers

PMID41331087
PMCPMC12818770

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.