Evidence map›Paper›PMID 42490500›Full record

ArticleScience (New York, N.Y.)2026

A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.

Yubao Cheng, Jianshu Wang, Yuan Zhang, Anurupa Devi Yadavalli, Miao Liu, Shengyan Jin, Grace Buddle, Ann Haberman, David G Schatz, Siyuan Wang

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2026. 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. 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

10 authors.

Yubao Cheng *Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0001-6967-1433
Jianshu Wang *Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
Yuan Zhang *Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.ORCID 0009-0003-6903-0427
Anurupa Devi YadavalliDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0003-4733-8028
Miao LiuDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0003-4248-2661
Shengyan JinDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0002-8667-7586
Grace BuddleDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
Ann HabermanDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0001-5168-8229
David G SchatzDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0002-5669-1176
Siyuan WangDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.ORCID 0000-0001-6550-4064

Funding

Yale SPORE in Lung Cancer (YSILC): The Biology and Personalized Treatment of Lung CancerP50CA196530 · NCI · YALE UNIVERSITY · PI Harriet M. Kluger · 2015 to 2026
$31.1M
Targeting of somatic hypermutation in the genomeR01AI127642 · NIAID · YALE UNIVERSITY · PI SCHATZ, DAVID G. · 2017 to 2025
$4.6M
Genome Architecture in Human Germinal Center B Cell Development, Malignancy, and Somatic HypermutationU01CA260701 · NCI · YALE UNIVERSITY · PI SCHATZ, DAVID G., WANG, SIYUAN · 2020 to 2024
$3.1M
Building the 3D genomic regulatomeDP2GM137414 · NIGMS · YALE UNIVERSITY · PI WANG, SIYUAN · 2019 to 2019
$2.5M
Spatial omics technologies to map the senescent cell microenvironmentUH3CA268202 · NCI · BROWN UNIVERSITY · PI MA, JIAN, NERETTI, NICOLA · 2023 to 2025
$2.2M
Multimodal Analysis of the Genome Architecture Using Expansion MicroscopyR01HG012969 · NHGRI · YALE UNIVERSITY · PI Joerg Bewersdorf, Antonio J Giraldez · 2024 to 2026
$2.1M
Integrative single-cell spatial genomic, transcriptomic, and epigenetic imaging in mammalian tissueR01HG011245 · NHGRI · YALE UNIVERSITY · PI WANG, SIYUAN · 2020 to 2023
$2.1M
3D genome reorganization drives cancer developmentR01CA292936 · NCI · YALE UNIVERSITY · PI Mandar Deepak Muzumdar, Siyuan Wang · 2024 to 2026
$2.1M
Developing next-generation high-content image-based genetic screens for multi-omic spatial phenotypesR01HG013503 · NHGRI · YALE UNIVERSITY · PI Siyuan Wang · 2024 to 2026
$2.0M
NCI NIH HHS P50 CA196530NCI NIH HHS R01 CA292936NCI NIH HHS U01 CA260701NCI NIH HHS UH3 CA268202NHGRI NIH HHS R01 HG011245NHGRI NIH HHS R01 HG012969NHGRI NIH HHS R01 HG013503NIAID NIH HHS R01 AI127642NIGMS NIH HHS DP2 GM137414
6 · The paper itself

Abstract

B cell maturation within the germinal center tissue microenvironment involves immunoglobulin gene diversification by somatic hypermutation (SHM). How three-dimensional (3D) genome architecture influences SHM is not fully understood. We leveraged sequencing-based and image-based 3D genomics and transcriptomics to map single-cell 3D genome organization and gene expression across cell types and states in human tonsils and in B cell lymphoma cell lines. These analyses revealed trajectories of compartment, looping, and nuclear position changes during the B cell immune response and activation of SHM. Targeted protein degradation of cohesin component RAD21 revealed its contribution to enabling SHM. Our results provide a single-cell 3D genome atlas of human tonsil cells and outline the links between the chromatin loop extrusion machinery and SHM.

Indexed as

B-LymphocytesChromatinGenome, HumanPalatine TonsilSomatic Hypermutation, ImmunoglobulinAtlases as TopicCell Cycle ProteinsCell Line, TumorCohesinsDNA-Binding ProteinsGerminal CenterHumansNuclear ProteinsSingle-Cell Gene Expression AnalysisCell Cycle ProteinsChromatinCohesinsDNA-Binding ProteinsNuclear Proteins

Identifiers

PMID42490500
PMCPMC13464094

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.