Abstract
Purpose :
Homeodomain transcription factors Six3 and its close paralog Six6 are co-expressed in mouse retinal progenitor cells. Our recent genetic study of Six3 and Six6 compound null retinas demonstrates that Six3 and Six6 are jointly required for retinal differentiation in mice. We hypothesize that Six3 and Six6 jointly activate or repress the transcription of their target genes in a context-dependent manner. This study aims to elucidate Six3- and Six6-regulated transcriptomes in embryonic mouse retinas at single-cell resolution.
Methods :
Six3 and Six6 compound null eyecups (Six3F/F;Six6-/-;a-Cre) and littermate controls (Six3+/-; Six6+/-) at embryonic day 13.5 (E13.5) were dissociated into single cells for single-cell RNA sequencing.
Results :
From control eyecups, 10,315 cells were sequenced at a depth of 21,726 reads / 2619 genes per cell. From Six3 and Six6 compound null eyecups, 12,672 cells were sequenced at a depth of 17,741 reads / 2330 genes per cell. The two datasets were integrated and analyzed using the Seurat package. Twenty cell clusters were identified. Compound null and control cells were mostly aligned in these clusters except for cluster 10, which was exclusively composed of compound null cells. Cell clusters for retinal progenitor cells, neurogenic cells, early differentiated neurons, and ciliary margin cells were identified. Markers for retinal progenitor cells were down-regulated, and markers for ciliary margins were up-regulated. Additionally, components of the Wnt signaling pathway were up-regulated in retinal progenitor cells and the cells that were specific for compound null cells. Target genes of Six3 and Six6 were identified.
Conclusions :
We identify Six3- and Six6-regulated transcriptomes in embryonic mouse eyecups at single-cell resolution.
This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.