A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate
The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important f...
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eLife Sciences Publications Ltd
2025-04-01
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| Online Access: | https://elifesciences.org/articles/102819 |
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| author | Eric R Brooks Andrew R Moorman Bhaswati Bhattacharya Ian S Prudhomme Max Land Heather L Alcorn Roshan Sharma Dana Pe'er Jennifer A Zallen |
| author_facet | Eric R Brooks Andrew R Moorman Bhaswati Bhattacharya Ian S Prudhomme Max Land Heather L Alcorn Roshan Sharma Dana Pe'er Jennifer A Zallen |
| author_sort | Eric R Brooks |
| collection | DOAJ |
| description | The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here, we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development. |
| format | Article |
| id | doaj-art-e21742cd107744848e49ec31f3d5e4de |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | eLife Sciences Publications Ltd |
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| series | eLife |
| spelling | doaj-art-e21742cd107744848e49ec31f3d5e4de2025-08-20T01:56:14ZengeLife Sciences Publications LtdeLife2050-084X2025-04-011310.7554/eLife.102819A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plateEric R Brooks0https://orcid.org/0000-0003-3159-8626Andrew R Moorman1Bhaswati Bhattacharya2Ian S Prudhomme3Max Land4Heather L Alcorn5Roshan Sharma6Dana Pe'er7Jennifer A Zallen8https://orcid.org/0000-0003-3975-1568Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, United States; Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Computational and Systems Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Computational and Systems Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Computational and Systems Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Computational and Systems Biology Program, Sloan Kettering Institute, New York, United StatesHoward Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, United StatesThe formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here, we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.https://elifesciences.org/articles/102819single-cell RNA sequencingmouse embryoneural platebrain developmentpatterningneural tube closure |
| spellingShingle | Eric R Brooks Andrew R Moorman Bhaswati Bhattacharya Ian S Prudhomme Max Land Heather L Alcorn Roshan Sharma Dana Pe'er Jennifer A Zallen A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate eLife single-cell RNA sequencing mouse embryo neural plate brain development patterning neural tube closure |
| title | A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| title_full | A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| title_fullStr | A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| title_full_unstemmed | A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| title_short | A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| title_sort | single cell atlas of spatial and temporal gene expression in the mouse cranial neural plate |
| topic | single-cell RNA sequencing mouse embryo neural plate brain development patterning neural tube closure |
| url | https://elifesciences.org/articles/102819 |
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