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

Abstract
Data availability
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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.

Data availability

Sequencing data have been deposited in GEO under accession GSE159107. Data can be visualized at the Broad Institute Single Cell Portal using the link: https://singlecell.broadinstitute.org/single_cell/study/SCP1159.

The following previously published data sets were used

1. Yan et al
(2020) human retina
NCBI Gene Expression Omnibus, GSE148077.

https://cdn.elifesciences.org/articles/63907/10:9802 10.1038/s41598-020-66092-9
1. Macasko et al
(2015) mouse rods
NCBI Gene Expression Omnibus, GSE63472.

https://cdn.elifesciences.org/articles/63907/10.1016/j.cell.2015.05.002
1. Shekhar et al
(2016) mouse bipolar
NCBI Gene Expression Omnibus, GSE81904.

https://cdn.elifesciences.org/articles/63907/10.1016/j.cell.2016.07.054
1. Yan et al
(2020) mouse amacrines
NCBI Gene Expression Omnibus, GSE149715.

https://cdn.elifesciences.org/articles/63907/10.1523/JNEUROSCI.0471-20.2020
1. Peng et al
(2019) macaque retina
NCBI Gene Expression Omnibus, GSE118852.

https://cdn.elifesciences.org/articles/63907/10.1016/j.cell.2019.01.004

Article and author information

Author details

Masahito Yamagata

Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8193-2931
Wenjun Yan

Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3568-4265
Joshua R Sanes

Molecular and Cellular Biology, Harvard University, Cambridge, United States

For correspondence
sanesj@mcb.harvard.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8926-8836

Funding

National Eye Institute (RO1EY022073)

Masahito Yamagata
Wenjun Yan
Joshua R Sanes

National Institute of Neurological Disorders and Stroke (NS029269)

Masahito Yamagata
Wenjun Yan
Joshua R Sanes

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#24-10) of Harvard University.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.