Fig. 1: BRN3B confers molecular identity to ipRGC subtypes.

A Differentially expressed transcripts in control and Brn3bcKO ipRGCs. B ipRGCs identified from publicly available scRNA-Seq profiles of RGCs³, re-analyzed using dimensionality reduction, and visualized with UMAP. Established genetic markers are used to annotate ipRGC subtypes. C Genes with increased and decreased expression in Brn3bcKO mice exhibited high variability in expression across ipRGC subtypes. DBrn3b and Opn4 mRNA levels in ipRGC subtypes. Relative expression of Opn4 and Brn3b mRNA in M1, M2, and M4 ipRGCs in scRNA-Seq dataset³. E Top genes that were enriched in M4, M5, and M6 ipRGCs with high levels of Brn3b expression (Brn3b^High) or in M1 and M2 ipRGC subtypes with low levels of Brn3b expression (Brn3b^Low)³. F Brn3bcKO induces opposite effects on transcripts found in Brn3b^Low and Brn3b^High ipRGCs (n = 50,57,164 transcripts for Brn3b^High, Brn3b^Low,all ipRGCs). Box plots show median, quartiles (box) and range (whiskers). G Volcano plot of Brn3bcKO-induced changes in transcript expression using TRAP. Transcriptional regulators which define ipRGC subtypes and are dysregulated in Brn3bcKO are highlighted. (H) Brn3bcKO-induced changes in Chrna6 and Zcchc12 transcript expression using TRAP (n = 4 mice/group). Data show mean ± standard error. I Schematic representation of RNAscope in flat-mount retinas. J Representative RNAscope pictures in flat mount retinas showing Chrna6 and Zcchc12 mRNA expression in putative M4 and M1 ipRGCs (dashed ellipses) in control (Opn4^Cre/+; Brn3b^+/+) and Brn3bcKO mice. K Relative expression of Chrna6 (P = 0.0001) and Zcchc12 (P = 0.0002) mRNA in ipRGCs from control (gray, n = 183 cells) and Brn3bcKO (green, n = 242 cells) mice measured by RNAscope. Pie plots show an increased number of ipRGCs expressing Zcchc12 mRNA in Brn3bcKO mice (P = 0.003). Source data are provided as a Source Data file. Lines are median values, **P < 0.01, ***P < 0.001, two-tailed Mann-Whitney U and Fisher’s exact tests.