Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum
The optic tectum (OT) is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus, the OT is responsible for the reception and integration of stimuli, followed by elicitation of salient behavioral responses....
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Molecular Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnmol.2022.818007/full |
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| author | Annalie Martin Anne Babbitt Allison G. Pickens Brett E. Pickett Jonathon T. Hill Arminda Suli |
| author_facet | Annalie Martin Anne Babbitt Allison G. Pickens Brett E. Pickett Jonathon T. Hill Arminda Suli |
| author_sort | Annalie Martin |
| collection | DOAJ |
| description | The optic tectum (OT) is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus, the OT is responsible for the reception and integration of stimuli, followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades, less is known concerning specific cell types, microcircuitry, and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however, a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single-cell RNA Sequencing (scRNA-seq) to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Et(cfos:Gal4;UAS:Kaede). We sequenced 13,320 cells, a 4X cellular coverage, and identified 25 putative OT cell populations. Within those cells, we identified several mature and developing neuronal populations, as well as non-neuronal cell types including oligodendrocytes and microglia. Although most mature neurons demonstrate GABAergic activity, several glutamatergic populations are present, as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes, and computed RNA velocity to infer current and future transcriptional cell states. Finally, we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion, the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge, this is the first time scRNA-seq has been applied to explore the OT alone and in depth. |
| first_indexed | 2024-12-24T01:51:36Z |
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| id | doaj.art-e411f9c6b7c64d2d9b52177cbbb327f6 |
| institution | Directory Open Access Journal |
| issn | 1662-5099 |
| language | English |
| last_indexed | 2024-12-24T01:51:36Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Neuroscience |
| spelling | doaj.art-e411f9c6b7c64d2d9b52177cbbb327f62022-12-21T17:21:44ZengFrontiers Media S.A.Frontiers in Molecular Neuroscience1662-50992022-02-011510.3389/fnmol.2022.818007818007Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic TectumAnnalie Martin0Anne Babbitt1Allison G. Pickens2Brett E. Pickett3Jonathon T. Hill4Arminda Suli5Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United StatesDepartment of Cell Biology and Physiology, Brigham Young University, Provo, UT, United StatesDepartment of Cell Biology and Physiology, Brigham Young University, Provo, UT, United StatesDepartment of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United StatesDepartment of Cell Biology and Physiology, Brigham Young University, Provo, UT, United StatesDepartment of Cell Biology and Physiology, Brigham Young University, Provo, UT, United StatesThe optic tectum (OT) is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus, the OT is responsible for the reception and integration of stimuli, followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades, less is known concerning specific cell types, microcircuitry, and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however, a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single-cell RNA Sequencing (scRNA-seq) to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Et(cfos:Gal4;UAS:Kaede). We sequenced 13,320 cells, a 4X cellular coverage, and identified 25 putative OT cell populations. Within those cells, we identified several mature and developing neuronal populations, as well as non-neuronal cell types including oligodendrocytes and microglia. Although most mature neurons demonstrate GABAergic activity, several glutamatergic populations are present, as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes, and computed RNA velocity to infer current and future transcriptional cell states. Finally, we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion, the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge, this is the first time scRNA-seq has been applied to explore the OT alone and in depth.https://www.frontiersin.org/articles/10.3389/fnmol.2022.818007/fulloptic tectumzebrafishmolecular characterizationsingle-cell RNA sequencingcell type identification |
| spellingShingle | Annalie Martin Anne Babbitt Allison G. Pickens Brett E. Pickett Jonathon T. Hill Arminda Suli Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum Frontiers in Molecular Neuroscience optic tectum zebrafish molecular characterization single-cell RNA sequencing cell type identification |
| title | Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum |
| title_full | Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum |
| title_fullStr | Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum |
| title_full_unstemmed | Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum |
| title_short | Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum |
| title_sort | single cell rna sequencing characterizes the molecular heterogeneity of the larval zebrafish optic tectum |
| topic | optic tectum zebrafish molecular characterization single-cell RNA sequencing cell type identification |
| url | https://www.frontiersin.org/articles/10.3389/fnmol.2022.818007/full |
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