ArticleScience (New York, N.Y.)2024
Massively parallel characterization of regulatory elements in the developing human cortex.
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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 44 papers.
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44citing papers in PubMed
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44 citing papers in PubMed.
- Article
- Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants.Nature neuroscience · 2026Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene FOXG1.Nature communications · 2026Article
- Massively parallel characterization and predictive modelling of neuronal regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- Integrative analyses elucidate transcriptional regulatory functions of risk alleles for metabolic liver disease.Nature genetics · 2026Article
- Massively parallel reporter assay-informed modeling improves prediction of context-specific enhancer-gene regulatory interactions.Nucleic acids research · 2026Article
- Regulatory risk loci link disrupted androgen response to the pathophysiology of polycystic ovary syndrome.Journal of the Endocrine Society · 2026Article
- Sex Differences in Brain Cell Type-Specific Chromatin Accessibility in Schizophrenia.Biological psychiatry · 2026Article
- Promoter mutagenesis and a massively parallel reporter screen of thebioRxiv : the preprint server for biology · 2026Article
- Silencer variants are key drivers of gene up-regulation in Alzheimer's disease.Science advances · 2026Article
- Multiplexed assays of variant effect for clinical variant interpretation.Nature reviews. Genetics · 2026Review
- Deep-learning prediction of gene expression from personal genomes.Genome biology · 2026Article
- Review
- MUSE: A Multi-slice Joint Analysis Method for Spatial Transcriptomics Experiments.Proceedings of the ... ACM International Conference on Information & Knowledge Management. ACM International Conference on Information and Knowledge Management · 2025Article
- Integrative functional genomics reveals transcriptional regulatory function of risk alleles for metabolic liver disease.Research square · 2025Article
- Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution.Nature communications · 2025Article
- Mapping causal non-coding variants in coronary artery disease.Nature cardiovascular research · 2025Article
- Predicting gene expression from DNA sequence using deep learning models.Nature reviews. Genetics · 2025Review
Corrections and comments
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Authors and funding
16 authors.
Chengyu Deng *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Sean Whalen *Gladstone Institutes, San Francisco, CA 94158, USA.
Marilyn SteyertDepartment of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
Ryan ZiffraDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Pawel F PrzytyckiGladstone Institutes, San Francisco, CA 94158, USA.
Fumitaka InoueInstitute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan.
Daniela A PereiraDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Davide CapautoChild Study Center, Yale University, New Haven, CT 06520, USA.
Scott NortonChild Study Center, Yale University, New Haven, CT 06520, USA.
Flora M VaccarinoChild Study Center, Yale University, New Haven, CT 06520, USA.
PsychENCODE Consortium‡
Alex A PollenKavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA.
Tomasz J NowakowskiDepartment of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
Nadav AhituvDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Katherine S PollardInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA.
PsychENCODE Consortium
Funding
Research Education ComponentP30AG066514 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Fanny M Elahi · 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
$29.9MPharmacogenomics of Membrane TransportersU19GM061390 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GIACOMINI, KATHLEEN M · 2010 to 2014
$16.3MMassively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systemsUM1HG011966 · NHGRI · UNIVERSITY OF WASHINGTON · PI Nadav Ahituv, Jay Ashok Shendure · 2021 to 2026
$9.7M 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
$7.6MMassively parallel reporter assays and genome editing of ENCODE predicted regulatory elementsUM1HG009408 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2017 to 2021
$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
$5.9MNHGRI NIH HHS UM1 HG009408NHGRI NIH HHS UM1 HG011966NIA NIH HHS P30 AG066514NIDA NIH HHS U01 DA048279NIDDK NIH HHS R01 DK124769NIGMS NIH HHS U19 GM061390NIMH NIH HHS DP2 MH122400NIMH 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 MH109907NIMH 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 MH116438NIMH 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 MH125246NIMH NIH HHS R01 MH125516NIMH NIH HHS R01 MH126393NIMH NIH HHS R01 MH126459NIMH NIH HHS R01 MH129301NIMH 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 MH122849NIMH NIH HHS UF1 MH130700NINDS NIH HHS R01 NS079231NINDS NIH HHS R01 NS123263
Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
Indexed as
Cerebral CortexNeurogenesisOrganoidsChromatinDeep LearningEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalHumansNeuronsPromoter Regions, GeneticRegulatory Elements, TranscriptionalRegulatory Sequences, Nucleic AcidChromatin
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