ArticleScience (New York, N.Y.)2024
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
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Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53citing papers in PubMed
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Who cites it
53 citing papers in PubMed.
- Identification of hub genes involved in early-onset schizophrenia: from genetic susceptibility to predicted regulated gene expression.Molecular psychiatry · 2026Article
- Spatiotemporal AI-based modeling of gene regulation and variant effects in the developing human brain using Seal.Nature neuroscience · 2026Article
- Review
- Single-nucleus atlas of cell-type specific genetic regulation in the human brain.Nature genetics · 2026Article
- Systems-Level Transcriptomic and Cellular Architecture of the Human Striatum in Schizophrenia and Bipolar Psychosis.Biology · 2026Article
- Estimating protein isoform abundances with [Formula: see text].Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Novel immune-related susceptibility loci associated with pediatric steroid-sensitive nephrotic syndrome identified by a transethnic genome-wide association study.Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
- Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo.Nature neuroscience · 2026Article
- Can Psychiatric Genetics Advance Without Incorporating a Life Course Perspective?Biological psychiatry · 2026Review
- Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.Cell genomics · 2026Article
- Downregulated transcription in chromosomal domains of midbrain dopamine neurons linked to schizophrenia.Nature communications · 2026Article
- Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function.Nature communications · 2026Article
- Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies.bioRxiv : the preprint server for biology · 2026Article
- Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age.bioRxiv : the preprint server for biology · 2026Article
- Integrating multi-omics and multi-context QTL data with GWAS reveals the genetic architecture of complex traits and improves the discovery of risk genes.medRxiv : the preprint server for health sciences · 2026Article
- A causal coding variant regulating alternative splicing ofScience advances · 2026Article
- The China Brain Multi-omics Atlas Project (CBMAP).Molecular psychiatry · 2026Review
Corrections and comments
- Update of
Authors and funding
39 authors.
Cindy WenInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0001-8747-8231
Michael MargolisDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0002-3706-8960
Rujia DaiDepartment of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA.ORCID 0000-0002-9979-3295
Pan ZhangDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0002-2233-9019
Pawel F PrzytyckiGladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA.ORCID 0000-0002-3360-6936
Daniel D VoDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0003-2057-969X
Arjun BhattacharyaDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0003-1196-4385
Nana MatobaDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.ORCID 0000-0001-5329-0134
Miao TangDepartment of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Chuan JiaoDepartment of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA.ORCID 0000-0002-8921-7841
Minsoo KimDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Ellen TsaiDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0002-9032-4011
Celine HohDepartment of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0009-0001-6896-125X
Nil AygünDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.ORCID 0000-0001-9766-0977
Rebecca L WalkerInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0003-1977-9547
Christos ChatzinakosDepartment of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.
Declan ClarkeDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-6128-7485
Henry PrattProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.ORCID 0000-0001-9413-834X
PsychENCODE Consortium†
Mette A PetersCNS Data Coordination Group, Sage Bionetworks, Seattle, WA 98109, USA.ORCID 0000-0001-7755-611X
Mark GersteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-9746-3719
Nikolaos P DaskalakisDepartment of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.ORCID 0000-0003-1660-9112
Zhiping WengProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.ORCID 0000-0002-3032-7966
Andrew E JaffeLieber Institute for Brain Development, Baltimore, MD 21205, USA.ORCID 0000-0001-6886-1454
Joel E KleinmanLieber Institute for Brain Development, Baltimore, MD 21205, USA.ORCID 0000-0002-4210-6052
Thomas M HydeLieber Institute for Brain Development, Baltimore, MD 21205, USA.ORCID 0000-0002-8746-3037
Daniel R WeinbergerLieber Institute for Brain Development, Baltimore, MD 21205, USA.ORCID 0000-0003-2409-2969
Nicholas J BrayMRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine, Cardiff CF24 4HQ, UK.ORCID 0000-0002-4357-574X
Nenad SestanDepartment of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.ORCID 0000-0003-0966-9619
Daniel H GeschwindDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0003-2896-3450
Kathryn RoederDepartment of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.ORCID 0000-0002-8869-6254
Alexander GusevDepartment of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.ORCID 0000-0002-7980-4620
Bogdan PasaniucInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Jason L SteinDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.ORCID 0000-0003-4829-0513
Michael I LoveDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Katherine S PollardGladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA.ORCID 0000-0002-9870-6196
Chunyu LiuDepartment of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA.ORCID 0000-0002-5986-4415
Michael J GandalInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0001-5800-5128
PsychENCODE Consortium
Funding
Research Education ComponentP30AG066514 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI NIKOLAOS K ROBAKIS · 2020 to 2026
$31.0MUCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M Functional Genomics of Human Brain DevelopmentP50MH106934 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2014 to 2019
$7.9MCis-Regulatory Epigenome Mappings in SchizophreniaU01MH103392 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, SKLAR, PAMELA · 2014 to 2017
$7.6MMolecular Profiling of SchizophreniaR01MH110921 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHESS, ANDREW J, ROUSSOS, PANAGIOTIS · 2016 to 2020
$6.9MTranscriptional and Epigenetic Signatures of Human Brain Development and AutismU01MH103339 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD, STATE, MATTHEW W. · 2014 to 2017
$6.5M1/2 Cell Type and Region-Specific Regulatory Networks in Human Brain Development and DisordersU01MH116488 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2018 to 2022
$6.5MDiscovery and validation of neuronal enhancers as development of psychiatric disorders supplementU01MH116492 · NIMH · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2018 to 2023
$6.2MThe 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorderU01MH116442 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, DRACHEVA, STELLA · 2018 to 2022
$5.9MUCLA-Caltech Medical Scientist Training ProgramT32GM152342 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Olujimi A Ajijola, David Wayne Dawson · 2024 to 2026
$5.3M2/3 Understanding PTSD through Postmortem Targeted Brain Multi-omicsR01MH117291 · NIMH · LIEBER INSTITUTE, INC. · PI Joel Edward Kleinman · 2018 to 2026
$5.2MSite 3/3, Understanding PTSD through Postmortem Targeted Brain MultiomicsR01MH117292 · NIMH · MCLEAN HOSPITAL · PI Nikolaos Daskalakis, KERRY J. RESSLER · 2018 to 2026
$5.0MNIA NIH HHS P30 AG066514NIDA NIH HHS U01 DA048279NIGMS NIH HHS T32 GM008042NIGMS NIH HHS T32 GM152342NIMH NIH HHS P50 MH106934NIMH NIH HHS R01 MH094714NIMH NIH HHS R01 MH105472NIMH NIH HHS R01 MH105898NIMH NIH HHS R01 MH109677NIMH NIH HHS R01 MH109715NIMH NIH HHS R01 MH110905NIMH NIH HHS R01 MH110920NIMH NIH HHS R01 MH110921NIMH NIH HHS R01 MH110926NIMH NIH HHS R01 MH110927NIMH NIH HHS R01 MH110928NIMH NIH HHS R01 MH111721NIMH NIH HHS R01 MH116529NIMH NIH HHS R01 MH117291NIMH NIH HHS R01 MH117292NIMH NIH HHS R01 MH117293NIMH NIH HHS R01 MH117406NIMH NIH HHS R01 MH121521NIMH NIH HHS R01 MH122681NIMH NIH HHS R01 MH123922NIMH NIH HHS R01 MH125516NIMH NIH HHS R01 MH126393NIMH NIH HHS R01 MH126459NIMH NIH HHS R01 MH129301NIMH NIH HHS R01 MH137578NIMH NIH HHS R21 MH102791NIMH NIH HHS R21 MH103877NIMH NIH HHS R21 MH105853NIMH NIH HHS R21 MH105881NIMH NIH HHS R21 MH109956NIMH NIH HHS R21 MH129817NIMH NIH HHS R56 MH114899NIMH NIH HHS R56 MH114901NIMH NIH HHS R56 MH114911NIMH NIH HHS U01 MH103339NIMH NIH HHS U01 MH103340NIMH NIH HHS U01 MH103346NIMH NIH HHS U01 MH103365NIMH NIH HHS U01 MH103392NIMH NIH HHS U01 MH116438NIMH NIH HHS U01 MH116441NIMH NIH HHS U01 MH116442NIMH NIH HHS U01 MH116487NIMH NIH HHS U01 MH116488NIMH NIH HHS U01 MH116489NIMH NIH HHS U01 MH116492NIMH NIH HHS U01 MH122509NIMH NIH HHS U01 MH122590NIMH NIH HHS U01 MH122591NIMH NIH HHS U01 MH122592NIMH NIH HHS U01 MH122678NIMH NIH HHS U01 MH122681NIMH NIH HHS U01 MH122849Wellcome Trust
Abstract
Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.
Indexed as
Alternative SplicingBrainGene Expression Regulation, DevelopmentalMental DisordersAtlases as TopicAutism Spectrum DisorderGene Regulatory NetworksGenome-Wide Association StudyHumansProtein IsoformsQuantitative Trait LociSchizophreniaTranscriptomeProtein Isoforms
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