Evidence map›Paper›PMID 40196612›Full record

ArticlebioRxiv : the preprint server for biology2025

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation.

Jingtian Zhou, Yue Wu, Hanqing Liu, Wei Tian, Rosa G Castanon, Anna Bartlett, Zuolong Zhang, Guocong Yao, Dengxiaoyu Shi, Ben Clock and 19 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

29 authors.

Jingtian ZhouArc Institute, Palo Alto, CA, USA.ORCID 0000-0003-2060-1922
Yue WuGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID 0009-0004-2428-0905
Hanqing LiuSociety of Fellows, Harvard University, Cambridge, MA, USA.ORCID 0000-0002-5114-6048
Wei TianGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID 0000-0002-2146-1717
Rosa G CastanonGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Anna BartlettGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Zuolong ZhangSchool of Software, Henan University, Kaifeng, Henan, China.
Guocong YaoSchool of Computer and Information Engineering, Henan University, Kaifeng, Henan, China.
Dengxiaoyu ShiGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Ben ClockGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Samantha MarcotteGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Joseph R NeryGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Michelle LiemFlow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA.
Naomi ClaffeyFlow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA.
Lara BoggemanFlow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA.
Cesar BarraganGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Rafael Arrojo E DrigoDepartment of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN.
Annika K WeimerDepartment of Genetics, Stanford School of Medicine, Stanford, CA, USA.
Minyi ShiDepartment of Genetics, Stanford School of Medicine, Stanford, CA, USA.
Johnathan Cooper-KnockSheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.ORCID 0000-0002-0873-8689
Sai ZhangDepartment of Genetics, Stanford School of Medicine, Stanford, CA, USA.
Michael P SnyderDepartment of Genetics, Stanford School of Medicine, Stanford, CA, USA.
Sebastian PreisslCenter for Epigenomics, University of California San Diego, La Jolla, CA, USA.
Bing RenCenter for Epigenomics, University of California San Diego, La Jolla, CA, USA.
Carolyn O'ConnorFlow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA.
Shengbo ChenSchool of Software, Nanchang University, Nanchang, Jiangxi, China.
Chongyuan LuoDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Jesse R DixonGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Joseph R EckerGenomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID 0000-0001-5799-5895

Funding

Center for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7M
Development of methods for multi-omic analysis of DNA methylation and chromatin architecture in single cellsR01HG010634 · NHGRI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI DIXON, JESSE R, ECKER, JOSEPH R · 2019 to 2022
$4.3M
Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomesU01CA260700 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI DIXON, JESSE R · 2020 to 2024
$3.5M
Spectral Configured Bigfoot Sorter for Salk Institute Flow Cytometry CoreS10OD034268 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI O'CONNOR, CAROLYN PEY-MIN · 2023 to 2023
$724k
BD FACSAria Fusion for Flow Cytometry Core FacilityS10OD023689 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI ZHENG, YE · 2018 to 2018
$530k
NCI NIH HHS U01 CA260700NHGRI NIH HHS R01 HG010634NHGRI NIH HHS UM1 HG011585NIH HHS S10 OD023689NIH HHS S10 OD034268Wellcome Trust
6 · The paper itself

Abstract

Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multi-omic profiling of 3D genome structure and DNA methylation for 86,689 single nuclei across 16 human tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across almost all cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Intriguingly, extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, indicating that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers an extensive reference for exploring gene regulation in human health and disease.

Identifiers

PMID40196612
PMCPMC11974725

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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.