Abstract
Purpose :
Epigenetic profiling of the structures of chromatin provides essential information about gene regulation. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) has been used to locate open chromatin sites, identify transcription regulatory regions, and determine positions of DNA-binding proteins. However, the epigenetic panorama remains incomplete for individual retinal cell types. To this aim, our study maps the open chromatin profiles and investigates the cell-type-specific regulatory elements in retinal single cells from three different species.
Methods :
Fresh retina samples from adult mice, non-human primates (marmoset and rhesus macaque), and human donors were processed using a single-cell assay for transposase-accessible chromatin. The data was analyzed by Cell Ranger pipelines and visualized with Loupe Cell Browser. Using SnapATAC, the cell populations were clustered according to chromatin accessibility and then identified by cell-specific gene markers.
Results :
Tens of thousands of cells have been sequenced for mouse, non-human primate and human retina. Cell marker gene analysis confirmed the high purity of the retina. Chromatin accessibility profiles of samples from macular and peripheral retina were broadly alike. Human and rhesus macaque retina showed similar chromatin accessibility profiles, and both had more open chromatin sites than the mouse retina. Cells from non-human primate and human retina have been clustered and identified as retinal major cell types. The peaks of fragments are enriched at the transcription start sites of cell-type-specific genes for corresponding clusters.
Conclusions :
Single-cell ATAC-seq is a promising tool that reveals rich epigenetic information. Our study analyzed open chromatin for cell-type identification and to specify potential transcription regulatory motifs. This data will provide an atlas of chromatin accessibility in retinal cells from the three key species and further advance our understanding of retina.
This is a 2020 ARVO Annual Meeting abstract.