A cell atlas of the chick retina based on single-cell transcriptomics

Abstract

Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. We used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. We identified 136 cell types plus 14 positional or developmental intermediates distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion, and glial cells. To assess morphology of molecularly defined types, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral, and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell, and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mouse, and primate retinal cell classes and types. Our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.

Expression of cell markers and transcription factors in the avian retina compared with that in the marmoset retina

“…Our quantification showed that in the central buzzard retina, 75–80% of all cells in the GCL were putative RGCs and many of these can be labeled by Satb1 and Foxp2 (Figure 7). However, transcriptomic data from Yamagata et al (2021) on the chicken retina suggest that there are at least 41 different types of RGCs. As staining for neurofilament labels α‐RGCs in many mammalian retinae (Krieger et al, 2017; Peichl et al, 1987) and α‐RGCs are conserved across many species, we analyzed NF200 labeling in the buzzard (Figure 8) and pigeon retina (Figure 9).…”

“…Transcriptomic and physiological studies revealed that amacrine and ganglion cells likely form >100 different cell types in the mouse retina (Baden et al, 2016; Rheaume et al, 2018; Yan et al, 2020) and recently, also for the chicken retina, ~100 amacrine and ganglion cells were reported (Yamagata et al, 2021). To characterize the inner retina of birds, we analyzed the expression of transcription factors and cellular markers (Table 3), determined cell densities in the GCL along the temporal‐nasal axis and compared the high‐acuity retinal regions of the buzzard with the primate.…”

“…Whether it labels an orthologous RGC type in the avian retina remains to be seen. Only very recently, Satb1 was shown to be expressed by many different types of RGCs in the chicken retina (Yamagata et al, 2021). In contrast, Satb2 showed a more restricted expression (Yamagata et al, 2021).…”

“…Only very recently, Satb1 was shown to be expressed by many different types of RGCs in the chicken retina (Yamagata et al, 2021). In contrast, Satb2 showed a more restricted expression (Yamagata et al, 2021). It was detected in monostratified RGCs of mice and primates (Dhande et al, 2019; Nasir‐Ahmad et al, 2021), in addition to bistratified ON–OFF direction‐selective RGCs of mice (Peng et al, 2017) and rabbits (Dhande et al, 2019), and bistratified RGCs of primates (Peng et al, 2019).…”

“…While the differential expression of various transcription factors is well established for some mammalian retinae (mostly mouse and primate), much less is known for avian retinae and only very recently, a cell atlas of the chick retina based on transcriptome analysis was provided (Yamagata et al, 2021). So far, most studies focused on the developmental role of transcription factors in the chick retina (Edqvist et al, 2006; Fischer et al, 2008) and not on their potential as markers for distinct cell types in the adult retina.…”