Abstract
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.
Highlights
The superior colliculus (SC) is a highly laminated multisensory processing hub located in the mammalian midbrain that receives sensory input of various modalities and is involved in visual, motor, and sensory pathways (Krauzlis et al, 2013; Stein and Stanford, 2013), as well as perceptual decision-making (Jun et al, 2021)
To preclude over-clustering based on technical noise, we identified clusters based upon the presence of marker genes meeting our diagnostic criteria and conclude that at 7 dpf the larval zebrafish brain contains at least 25 transcriptionally distinct cell populations
To compliment current tectal characterization efforts, we describe the transcriptomic profiles for 25 molecularly distinct tectal cell populations including novel marker genes, neurotransmitter identities, potential synaptic partners, transcription factor expression, and developmental predictions
Summary
The superior colliculus (SC) is a highly laminated multisensory processing hub located in the mammalian midbrain that receives sensory input of various modalities and is involved in visual, motor, and sensory pathways (Krauzlis et al, 2013; Stein and Stanford, 2013), as well as perceptual decision-making (Jun et al, 2021). Similar to the mammalian SC, the OT has the critical role of receiving sensory input. It is responsible for visually guided behaviors such as phototaxis, prey capture, obstacle avoidance, and predator escape (Wong, 1999; Gahtan et al, 2005; Nevin et al, 2008, 2010; Fero et al, 2011; Lowe et al, 2013; Vanwalleghem et al, 2017). The tectum can be broadly divided into two regions: the periventricular layer (PVL), where the majority of tectal cell bodies lie; and the neuropil (NP), which consists primarily of neurites. A hypothalamic influence on the OT has been uncovered, as neurons within the rostral hypothalamus project to the SFGS and an area between the SGC and SAC (Heap et al, 2018)
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