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A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
- Source :
- Nature Communications, 12(1), Nature Communications, 12(1). NATURE RESEARCH, Joglekar, A, Prjibelski, A, Mahfouz, A, Collier, P, Lin, S, Schlusche, A K, Marrocco, J, Williams, S R, Haase, B, Hayes, A, Chew, J G, Weisenfeld, N I, Wong, M Y, Stein, A N, Hardwick, S A, Hunt, T, Wang, Q, Dieterich, C, Bent, Z, Fedrigo, O, Sloan, S A, Risso, D, Jarvis, E D, Flicek, P, Luo, W, Pitt, G S, Frankish, A, Smit, A B, Ross, M E & Tilgner, H U 2021, ' A spatially resolved brain region-and cell type-specific isoform atlas of the postnatal mouse brain ', Nature Communications, vol. 12, 463, pp. 1-16 . https://doi.org/10.1038/s41467-020-20343-5, Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021), Nature Communications, Nature Communications, 12:463, 1-16. Nature Publishing Group
- Publication Year :
- 2021
-
Abstract
- Splicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 (www.isoformAtlas.com). Isoform tests for DIE show better performance than exon tests. We detect hundreds of DIE events traceable to cell types, often corresponding to functionally distinct protein isoforms. Mostly, one cell type is responsible for brain-region specific DIE. However, for fewer genes, multiple cell types influence DIE. Thus, regional identity can, although rarely, override cell-type specificity. Cell types indigenous to one anatomic structure display distinctive DIE, e.g. the choroid plexus epithelium manifests distinct transcription-start-site usage. Spatial transcriptomics and long-read sequencing yield a spatially resolved splicing map. Our methods quantify isoform expression with cell-type and spatial resolution and it contributes to further our understanding of how the brain integrates molecular and cellular complexity.<br />Alternative RNA splicing varies across the brain. Its mapping at single cell resolution is unclear. Here, the authors provide a spatial and single-cell splicing atlas reporting brain region- and cell type-specific expression of different isoforms in the postnatal mouse brain.
- Subjects :
- 0301 basic medicine
Gene isoform
Cell type
RNA splicing
Science
General Physics and Astronomy
Prefrontal Cortex
Biology
Hippocampus
General Biochemistry, Genetics and Molecular Biology
Article
Transcriptome
03 medical and health sciences
Exon
Mice
0302 clinical medicine
Animals
Protein Isoforms
Prefrontal cortex
Transcriptomics
Gene
Regulation of gene expression
Spatial Analysis
Multidisciplinary
Computational Biology
Gene Expression Regulation, Developmental
Development of the nervous system
General Chemistry
Cell biology
Alternative Splicing
030104 developmental biology
Animals, Newborn
Computational neuroscience
Models, Animal
Female
Single-Cell Analysis
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Database :
- OpenAIRE
- Journal :
- Nature Communications, 12(1), Nature Communications, 12(1). NATURE RESEARCH, Joglekar, A, Prjibelski, A, Mahfouz, A, Collier, P, Lin, S, Schlusche, A K, Marrocco, J, Williams, S R, Haase, B, Hayes, A, Chew, J G, Weisenfeld, N I, Wong, M Y, Stein, A N, Hardwick, S A, Hunt, T, Wang, Q, Dieterich, C, Bent, Z, Fedrigo, O, Sloan, S A, Risso, D, Jarvis, E D, Flicek, P, Luo, W, Pitt, G S, Frankish, A, Smit, A B, Ross, M E & Tilgner, H U 2021, ' A spatially resolved brain region-and cell type-specific isoform atlas of the postnatal mouse brain ', Nature Communications, vol. 12, 463, pp. 1-16 . https://doi.org/10.1038/s41467-020-20343-5, Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021), Nature Communications, Nature Communications, 12:463, 1-16. Nature Publishing Group
- Accession number :
- edsair.doi.dedup.....7712a28f4e2e541325f3f669a7004ac3
- Full Text :
- https://doi.org/10.1038/s41467-020-20343-5