Single cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration

In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single cell RNA sequencing of Müller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Müller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Müller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Müller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans. Droplet-based, 10x Genomics scRNAseq was done on four samples. Each sample consists of 15000 cells sorted from a single cell suspension obtained by dissociating 8 retinae pooled from the eyes of 4, adult zebrafish (2 males and 2 females). Samples were collected from light-lesioned animals at 44 hours post-light lesion (hpl) (s2_44_hpl_), 4 and 6 days post-light lesion (dpl) (s3_4_dpl_ and s5_6_dpl_, respectively). Two, separate uninjured control samples included cells dissociated from 8 retinae of 4, uninjured zebrafish (s1_Uninjured_Ch_ and s4_Uninjured_whole_retina_ctrl_, respectively). Sample collection occurred on two, different working days. On the first day, s1_Uninjured_Ch_, s2_44_hpl_ and s3_4_dpl_ were collected. On the second day, s4_Uninjured_whole_retina_ctrl_ and s5_6_dpl_ were collected. Fluorescent Activated Cell Sorting (FACS) was applied to each sample and eventually 15.000 cells per sample were sorted and sent for sequencing.