The SoxC transcription factors regulate multiple early retinal lineages and function in parallel with Atoh7 to promote retinal ganglion cell genesis

Retinal development is orchestrated by a network of transcription factors that guide multipotent retinal progenitor cells (RPCs) to fate-committed lineages, ultimately producing seven major retinal cell classes. Among these, retinal ganglion cells (RGCs) serve as the sole output neurons of the retina, relaying visual and non-visual information to the brain. RGC specification requires a cascade of transcriptional regulators, including the basic helix-loop-helix (bHLH) factor Atoh7, which confers competence to RPCs, and Pou4f2 and Isl1, which drive terminal differentiation and subtype diversification. Previous studies demonstrate that the SoxC group transcription factors (Sox4, Sox11, and Sox12) are also involved in RGC genesis, but their precise integration into the Atoh7-driven regulatory hierarchy remains undefined. To address this question, we used the retina-specific Vsx2-Cre line to generate Sox4/Sox11 double conditional knockout (dcKO) and Sox4/Sox11/Atoh7 triple knockout (tKO) mice. Immunohistochemistry revealed profound lineage disruption and reduced progenitor proliferation and survival in both dcKO and tKO retinas; not only RGC genesis but also that of horizontal and amacrine (H&As) cells were severely compromised, whereas photoreceptor cells (PHCs) production increased. These results indicate that Sox4 and Sox11 are involved in the coordinated generation of the different early retinal lineages. Like the Atoh7-null retina, RGC precursors still formed in the SoxC dcKO retina, but their genesis was almost completely abolished in the tKO retina. Our findings indicate that the SoxC factors act in parallel with Atoh7 as a major upstream regulatory input to initiate RGC fate. Bulk RNA-seq revealed the SoxC-dependent transcriptional programs and signaling pathways and confirmed the lineage changes demonstrated by marker analysis. CUT&Tag analysis identified the genome-wide binding sites and thereby the target genes of Sox11, further illuminating the mechanisms underlying functions of the SoxC factors in multiple retinal cell states/types during development.