ArticleProceedings of the National Academy of Sciences of the United States of America2021
Transcriptional network orchestrating regional patterning of cortical progenitors.
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Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40citing papers in PubMed
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Who cites it
40 citing papers in PubMed.
- TheiScience · 2026Article
- Temporal control of midline crossing via incoherent feedforward and feedback loops regulating Robo3.iScience · 2026Article
- R-loop landscapes in the developing human brain are linked to neural differentiation and cell type-specific transcription.Translational psychiatry · 2026Article
- An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors.Developmental biology · 2026Article
- Identifying key regulators in neuronal transdifferentiation by gene regulatory network analysis.PNAS nexus · 2025Article
- Temporal control of axonal floor plate crossing through a combination of incoherent feedforward and feedback loops of gene regulatory network regulating Robo3 expression.bioRxiv : the preprint server for biology · 2025Article
- Article
- Engineering human neuronal diversity: Morphogens and stem cell technologies for neurodevelopmental biology.Stem cell reports · 2025Review
- Outcrossing Complicates Mutation Purging by Trapping Single Nucleotide Polymorphisms in Structural Variant Mutations.bioRxiv : the preprint server for biology · 2025Article
- A developmental gradient of COUP-TFI expression regulates the relative size of hippocampus dorsal and ventral subregions.PLoS biology · 2025Article
- Novel Insights into Emx2 and Dmrta2 Cooperation during Cortex Development and Evidence for Dmrta2 Function in the Choroid Plexus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Evidence That Dmrta2 Acts through Repression ofeNeuro · 2025Article
- The Principle of Cortical Development and Evolution.Neuroscience bulletin · 2025Review
- Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.Developmental cell · 2025Article
- Molecular signatures of cortical expansion in the human foetal brain.Nature communications · 2024Article
- Identifying genetic variants that influence the abundance of cell states in single-cell data.Nature genetics · 2024Article
- Article
- Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation.BMC biology · 2024Article
- Deciphering the functional specialization of whole-brain spatiomolecular gradients in the adult brain.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms.Science (New York, N.Y.) · 2024Article
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Authors and funding
20 authors.
Athéna R YpsilantiNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158; athena.ypsilanti@ucsf.edu john.rubenstein@ucsf.edu.ORCID 0000-0002-0310-7693
Kartik PattabiramanNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.ORCID 0000-0002-3924-426X
Rinaldo Catta-PretaDepartment of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618.ORCID 0000-0001-9833-1278
Olga GolonzhkaNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.
Susan LindtnerNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.
Ke TangPrecise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.ORCID 0000-0002-0516-4667
Ian R JonesInstitute for Human Genetics, University of California, San Francisco, CA 94143.
Armen AbnousiDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
Ivan JuricDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
Ming HuDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.ORCID 0000-0003-0987-2916
Yin ShenInstitute for Human Genetics, University of California, San Francisco, CA 94143.
Diane E DickelEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Axel ViselEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Len A PennachioEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Michael HawrylyczAllen Institute for Brain Science, Seattle, WA 98109.
Carol L ThompsonAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1528-3237
Hongkui ZengAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-0326-5878
Iros BarozziFaculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, United Kingdom.ORCID 0000-0003-0690-3473
Alex S NordDepartment of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618.ORCID 0000-0003-4259-7514
John L RubensteinNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158; athena.ypsilanti@ucsf.edu john.rubenstein@ucsf.edu.ORCID 0000-0002-4414-7667
Funding
Translational InformaticsP30CA082103 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Kate Taylor Shumate · 1999 to 2026
$209.7MGeneration of an In Vivo Human Genome Transcriptional Enhancer DatasetR01HG003988 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Len Alexander Pennacchio · 2006 to 2026
$24.1MSan Diego Center for 4D Nucleome ResearchU54DK107977 · NIDDK · LUDWIG INSTITUTE FOR CANCER RES LTD · PI REN, BING · 2015 to 2019
$9.4MPHARMACEUTICAL SCIENCES AND PHARMACOGENOMICST32GM007175 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, KROETZ, DEANNA L · 1985 to 2021
$7.1MGenetic Studies of Cortex Structure and DevelopmentR01NS099099 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 2016 to 2025
$6.4MGenetic Regulation of Telencephalon DevelopmentR37MH049428 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 2008 to 2017
$5.9MSTRUCTURE, EXPRESSION &FUNCTION OF THE DLX GENE FAMILYR01MH049428 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 1992 to 2022
$5.8MGENETIC STUDIES OF CORTEX STRUCTURE AND DEVELOPMENTR01NS034661 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 1996 to 2015
$4.6MFunctional Elucidation of the Sequence-Encoded Regulatory Activity of Enhancers in Vivo in the BrainR35GM119831 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Alexander Nord · 2016 to 2026
$3.9MNCI NIH HHS P30 CA082103NHGRI NIH HHS R01 HG003988NIDDK NIH HHS U54 DK107977NIGMS NIH HHS R35 GM119831NIGMS NIH HHS T32 GM007175NIMH NIH HHS R01 MH049428NIMH NIH HHS R37 MH049428NINDS NIH HHS R01 NS034661NINDS NIH HHS R01 NS099099
Abstract
We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (
Indexed as
Gene Regulatory NetworksRegulatory Elements, TranscriptionalAnimalsCerebral CortexCOUP Transcription Factor IEmpty Spiracles Homeobox ProteinsEpigenomeHomeodomain ProteinsLIM-Homeodomain ProteinsMicePAX6 Transcription FactorPre-B-Cell Leukemia Transcription Factor 1Transcription FactorsCOUP Transcription Factor IEmpty Spiracles Homeobox ProteinsHomeodomain ProteinsLhx2 protein, mouseLIM-Homeodomain ProteinsNr2f1 protein, mousePax6 protein, mousePAX6 Transcription FactorPbx1 protein, mousePre-B-Cell Leukemia Transcription Factor 1Transcription Factorscortical patterningepigeneticsprogenitor cellstranscription factors
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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.