Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [10x multiome]

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE). We identified 420,824 unique candidate regulatory elements and characterized their chromatin state in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina, leading to mechanistic insights into a wide-spectrum of eye diseases. The eye globes were collected from three unrelated human donors (aged 21, 27 and 43 years) (Table-X) with the collaboration of San Diego Eye Bank. The sample processing time starting from eye enucleation to dissection was restricted within 2 hours to identify the macula, a visible yellowish/whiteish indent that is slightly lateral to the optic disk inside the globe. Prior dissection, the eye globe with proper label was collected in a sterile moist chamber. At first the cornea was removed by cutting 2-3 mm around the limbus using a surgical blade. Pull off the iris and lens. This will leave you with the eye cup, which contains the posterior pole. After removing enough vitreous and aqueous fluid the temporal region can be located by two main blood vessels that curl around the macula. Using a sterile 3mm skin biopsy punch, the macula was collected. Sections were made for the other regions, temporal, nasal, superior and inferior. For all these regions, the retina and RPE tissue were separated and stored immediately in Liquid Nitrogen.