Evidence map›Paper›PMID 41676679›Full record

ArticlebioRxiv : the preprint server for biology2026

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain.

Yang Xie, Lei Chang, Guojie Zhong, Jonathan A Rink, Tatiana Báez-Becerra, Ethan Armand, Wubin Ding, Kai Li, Eric Bonne, Audrey Lie and 45 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

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

55 authors.

Yang XieNew York Genome Center, New York, NY, USA.ORCID 0000-0002-7453-6786
Lei ChangNew York Genome Center, New York, NY, USA.
Guojie ZhongNew York Genome Center, New York, NY, USA.
Jonathan A RinkComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Tatiana Báez-BecerraComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Ethan ArmandDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Wubin DingGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Kai LiDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Eric BonneCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Audrey LieDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Hannah S IndralingamDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Keyi DongDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Timothy LoeDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Bohan HuangDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Zhaoning WangDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Ariana S BarcomaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jackson K WillierComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Kyle W KnutsonComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jiayi LiuComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Silvia ChoComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Stella CaoComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Kaitlyn G RussoComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Carissa K YoungComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jessica ArzavalaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Yareli SanchezComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Aleksandra BikkinaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Natalie Schenker-AhmedGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Colin KernCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Zoey ZhaoCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Amit KleinGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jesus FloresCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Chu-Yi TaiCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Jacqueline OlnessCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Alexander MonellCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Siavash MoghadamiCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Cesar BarraganGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Chumo ChenGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
William OwensGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Carolyn O'ConnorFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Michelle LiemFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Mikayla V MarrinFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Cynthia RoseFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Shane N AltFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Nora EmersonComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Julia OsteenComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jacinta LuceroComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Daofeng LiDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Rebecca D HodgeAllen Institute for Brain Science, Seattle, WA, USA.
Ting WangDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
C Dirk KeeneDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA.
Xiangming XuDepartment of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
Quan ZhuCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
M Margarita BehrensComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Bing RenNew York Genome Center, New York, NY, USA.

Funding

Center for Multiomic Human Brain Cell AtlasUM1MH130994 · NIMH · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI MARIA MARGARITA BEHRENS, Joseph R Ecker · 2022 to 2026
$92.4M
University of Washington Alzheimer's Disease Research CenterP30AG066509 · NIA · UNIVERSITY OF WASHINGTON · PI Amanda D. Boyd · 2020 to 2026
$29.0M
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
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
BD FACSAria Fusion for Flow Cytometry Core FacilityS10OD023689 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI ZHENG, YE · 2018 to 2018
$530k
NIA NIH HHS P30 AG066509NIH HHS S10 OD023689NIH HHS S10 OD026929NIH HHS S10 OD034268NIMH NIH HHS UM1 MH130994
6 · The paper itself

Abstract

Directly measuring chromatin states alongside transcription is essential for understanding how cell-type-specific regulatory programs are established and maintained in the adult human brain. We present a large-scale single-cell multimodal atlas generated by jointly profiling transcriptome with active (H3K27ac) and repressive (H3K27me3) histone modifications across 18 brain regions. We profile >750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization.

Indexed as

chromatin statehistone acetylationneuropsychiatric geneticsPolycomb repressionSingle-nucleus multi-omicsspatial transcriptome

Identifiers

PMID41676679
PMCPMC12889664

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LicenceCC BY-NC-ND
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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.