Alternative splicing across the C. elegans nervous system
Abstract Alternative splicing is a key mechanism that shapes transcriptomes, helping to define neuronal identity and modulate function. Here, we present an atlas of alternative splicing across the nervous system of Caenorhabditis elegans. Our analysis identifies novel alternative splicing in key neu...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-58293-5 |
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| author | Alexis Weinreb Erdem Varol Alec Barrett Rebecca M. McWhirter Seth R. Taylor Isabel Courtney Manasa Basavaraju Abigail Poff John A. Tipps Becca Collings The CeNGEN Consortium Smita Krishnaswamy David M. Miller Marc Hammarlund |
| author_facet | Alexis Weinreb Erdem Varol Alec Barrett Rebecca M. McWhirter Seth R. Taylor Isabel Courtney Manasa Basavaraju Abigail Poff John A. Tipps Becca Collings The CeNGEN Consortium Smita Krishnaswamy David M. Miller Marc Hammarlund |
| author_sort | Alexis Weinreb |
| collection | DOAJ |
| description | Abstract Alternative splicing is a key mechanism that shapes transcriptomes, helping to define neuronal identity and modulate function. Here, we present an atlas of alternative splicing across the nervous system of Caenorhabditis elegans. Our analysis identifies novel alternative splicing in key neuronal genes such as unc-40/DCC and sax-3/ROBO. Globally, we delineate patterns of differential alternative splicing in almost 2000 genes, and estimate that a quarter of neuronal genes undergo differential splicing. We introduce a web interface for examination of splicing patterns across neuron types. We explore the relationship between neuron type and splicing, and between splicing and differential gene expression. We identify RNA features that correlate with differential alternative splicing and describe the enrichment of microexons. Finally, we compute a splicing regulatory network that can be used to generate hypotheses on the regulation and targets of alternative splicing in neurons. |
| format | Article |
| id | doaj-art-8ff62b5727d24ebbaabed5513d22b5ad |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-8ff62b5727d24ebbaabed5513d22b5ad2025-08-20T02:25:16ZengNature PortfolioNature Communications2041-17232025-05-0116112110.1038/s41467-025-58293-5Alternative splicing across the C. elegans nervous systemAlexis Weinreb0Erdem Varol1Alec Barrett2Rebecca M. McWhirter3Seth R. Taylor4Isabel Courtney5Manasa Basavaraju6Abigail Poff7John A. Tipps8Becca Collings9The CeNGEN ConsortiumSmita Krishnaswamy10David M. Miller11Marc Hammarlund12Department of Genetics, Yale University School of MedicineTandon School of Engineering, New York UniversityDepartment of Genetics, Yale University School of MedicineDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Genetics, Yale University School of MedicineDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Genetics, Yale University School of MedicineDepartment of Cell and Developmental Biology, Vanderbilt UniversityDepartment of Genetics, Yale University School of MedicineAbstract Alternative splicing is a key mechanism that shapes transcriptomes, helping to define neuronal identity and modulate function. Here, we present an atlas of alternative splicing across the nervous system of Caenorhabditis elegans. Our analysis identifies novel alternative splicing in key neuronal genes such as unc-40/DCC and sax-3/ROBO. Globally, we delineate patterns of differential alternative splicing in almost 2000 genes, and estimate that a quarter of neuronal genes undergo differential splicing. We introduce a web interface for examination of splicing patterns across neuron types. We explore the relationship between neuron type and splicing, and between splicing and differential gene expression. We identify RNA features that correlate with differential alternative splicing and describe the enrichment of microexons. Finally, we compute a splicing regulatory network that can be used to generate hypotheses on the regulation and targets of alternative splicing in neurons.https://doi.org/10.1038/s41467-025-58293-5 |
| spellingShingle | Alexis Weinreb Erdem Varol Alec Barrett Rebecca M. McWhirter Seth R. Taylor Isabel Courtney Manasa Basavaraju Abigail Poff John A. Tipps Becca Collings The CeNGEN Consortium Smita Krishnaswamy David M. Miller Marc Hammarlund Alternative splicing across the C. elegans nervous system Nature Communications |
| title | Alternative splicing across the C. elegans nervous system |
| title_full | Alternative splicing across the C. elegans nervous system |
| title_fullStr | Alternative splicing across the C. elegans nervous system |
| title_full_unstemmed | Alternative splicing across the C. elegans nervous system |
| title_short | Alternative splicing across the C. elegans nervous system |
| title_sort | alternative splicing across the c elegans nervous system |
| url | https://doi.org/10.1038/s41467-025-58293-5 |
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