Evidence map›Paper›PMID 41659519›Full record

ArticlebioRxiv : the preprint server for biology2026

A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons.

Matthew G Heffel, Heng Xu, Oier Pastor-Alonso, Xinzhe Li, Mohammad S Baig, Rayyan Irfan Ghoor, Runjia Li, Colin Kern, Joonho Kum, Yi Zhang and 26 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

36 authors.

Matthew G HeffelDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Heng XuDepartment of Cognitive Science, University of California San Diego, La Jolla, CA 92093, USA.
Oier Pastor-AlonsoDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Xinzhe LiGenomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
Mohammad S BaigDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Rayyan Irfan GhoorDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Runjia LiBioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA.
Colin KernCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Joonho KumDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Yi ZhangDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Jon PainoDepartment of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.
Min Jen TsaiDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Chu-Yi TaiCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Grant TuckerCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Zoey ZhaoCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Angie HouCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Zachary von BehrenDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Mohini BhadeDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Siqian LiDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Kadellyn SandovalDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Jessica ScholesEli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
Felicia CodreaEli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
Jeffrey CalimlimEli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
Emma K LiaoDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
Gwyneth LeungDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
JaeYeon KimDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Eleazar EskinDepartment of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
Jonathan FlintDepartment of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0002-9427-4429
Jennifer A CotterDepartment of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
Bogdan PasaniucDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Bogdan BintuDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
Quan ZhuCenter for Epigenomics, University of California San Diego, La Jolla, CA 92093, USA.
Eran A MukamelDepartment of Cognitive Science, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0003-3203-9535
Jason ErnstDepartment of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.
Mercedes F ParedesDepartment of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
Chongyuan LuoDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.

Funding

UCLA IDDRC: Translational CoreP50HD103557 · NICHD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SAMANTHA J BUTLER · 2020 to 2026
$9.6M
Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotencyU01HG012079 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Kathrin Plath · 2021 to 2026
$6.9M
Spatiotemporal epigenomic and chromosomal architectural cell atlas of developing human brainsU01MH130995 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Mercedes Paredes · 2022 to 2026
$4.4M
SINGLE-CELL MULTI-OMIC APPROACHES TO MECHANISTICALLY CHARACTERIZE PSYCHIATRIC DISORDER RISK LOCI IN THE HUMAN BRAINR01MH125252 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUO, CHONGYUAN · 2021 to 2025
$3.7M
High-throughput imaging of 3D chromatin regulation events in the nervous systemDP5OD031878 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BINTU, BOGDAN · 2021 to 2025
$2.0M
In situ Single-Cell Multi-Omic and Morphological Profiling in Mammalian BrainsRF1MH130461 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUO, CHONGYUAN · 2022 to 2022
$1.8M
Protracted Maturation of Cortical Inhibitory Neurons for the Complexity of Higher Cognitive AreasK99NS138587 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Jaeyeon Kim · 2025 to 2026
$231k
NHGRI NIH HHS U01 HG012079NICHD NIH HHS P50 HD103557NIH HHS DP5 OD031878NIMH NIH HHS R01 MH125252NIMH NIH HHS RF1 MH130461NIMH NIH HHS U01 MH130995NINDS NIH HHS K99 NS138587
6 · The paper itself

Abstract

The human basal ganglia (BG), subcortical nuclei fundamental to motor regulation and cognitive modulation, is constructed from neurons produced during gestation in the adjacent ganglionic eminences (GEs). GEs are transient structures in the ventral prenatal brain that also generate GABAergic inhibitory neurons which migrate to destinations in the BG, cortex and other destinations. This study aims to elucidate the epigenomic and 3D-genomic dynamics involved in the specification and maturation of GEs and GE-derived neurons, using single-nucleus methyl-3C sequencing (snm3C-seq), highly-multiplexed spatial transcriptomics, and chromatin+RNA single-molecule imaging. Our multi-modal data support a heterogeneous temporal progression across GE subregions, with the lateral GE (LGE) showing declining neurogenic activity in mid-gestation and caudal GE (CGE) exhibiting ongoing developmental progression through infancy. We identified regulatory programs that specify subtypes of BG principal cells, medium spiny neurons (MSN), via synchronized maturation of the 3D-epigenome. In infant brains, we found a transient short-range enriched (SE) chromatin conformation during the transition between oligodendrocyte progenitors (OPCs) and oligodendrocytes (ODCs), and a temporary shift toward Long-range Enriched (LE) chromatin conformation in projection neurons, extending previous works showing the differentiation of neurons and glial cells is associated with permanent SE and LE conformation, respectively. Lastly, we found that gene regulatory regions active in MSNs were enriched in loci associated with genetic risk for neuropsychiatric disease. Our study delineates the highly complex, lineage-specific 3D genomic dynamics in ventral progenitors and basal ganglia populations of the perinatal human brain.

Identifiers

PMID41659519
PMCPMC12874046

What Socratic 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 Socratic graph.