GSE210414
The transcriptional networks governing the spatial regulation of RPE differentiation are regulated by the SWI/SNF complexes
During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to assure the gradual, coordinated differentiation of multiple lineages. Here, we study this  regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function, and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme, obtained by geographic positional sequencing (Geo-Seq) of a single development stage of the eye, encompassing young and more mature ocular progenitors. These transcriptomic data, available through an online web tool, reveal the major transcription factors and their gene regulatory networks that control over 5000 genes during RPE and ocular mesenchyme differentiation. We also present evidence, based on conditional inactivation followed by Geo-seq, that this differentiation program is dependent on the activity of the SWI/SNF complexes. We find that these complexes are required for the expression and activity of the RPE TFs and inhibition of the competing, default neuronal progenitor phenotypes and cell proliferation genes. The persistent expression of proliferation genes, despite onset of neurogenesis upon loss of SWI/SNF supports the tumor suppressive activity of these complexes. Our work reveals that the TFs regulation of a timely, gradual differentiation program, as well as maintenance of cell fate and ensuring exit from the cell cycle, depends on the chromatin terrine defined by the SWI/SNF chromatin remodelers. Overall design: We used spatial transcriptomic of Geo-Seq analyses of the embryonic  retinal pigmented epithelium (R/PE) and ocular mesenchyme (M/Me). We collected  samples lengths ranging from 180 to 450µm from the PE and Me  by laser capture microscopy (LCM), from 20um cryosections of E14.5 embryonic mouse eyes.  From each tissue (PE or Me) we collected a total of 8 samples: 4 samples were from the dorsal and 4 from the ventral optic cup along the proximal-distal axis.  We used this design to collect samples from 4 control (C) embryos and 3 conditional mutants in the PE, of both Smarcc1 and Smarcc2 (Smarcc1 loxP/loxP; Smarcc2loxP/loxP;DCT-Cre termed FcKO/F). We constructed from the data a high resolution spatial transcriptomic atlas of the developing PE and Me lineages in the control and in the FcKO.