Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2

The meninges act as a regulator of brain development by secreting ligands that act on neural cells to regulate neurogenesis and neuronal migration. Meningeal-derived retinoic acid (RA) promotes neocortical neural progenitor cell cycle exit; however, the underlying molecular mechanism is unknown. Here, we used spatial transcriptomics and profiling of retinoic-acid receptor-α (RARα) DNA binding in Foxc1-mutant embryos that lack meninges-derived ligands to identify the neurogenic transcriptional mechanisms of RA signaling in telencephalic neural progenitors. We determined that meningeal-derived RA controls neurogenesis by suppressing progenitor self-renewal pathways Notch signaling and the transcription factor Sox2. We show that RARα binds in the Sox2ot promoter, a long non-coding RNA that regulates Sox2expression, and RA promotes Sox2ot expression in neocortical progenitors. Our findings elucidate a previously unknown mechanism of how meningeal RA coordinates neocortical development and i..., Pregnant mice were anesthetized using isoflurane and embryos were collected at E12, E13, or E14 by removing the heads and placing them in 4% paraformaldehyde (PFA) overnight at 4 degrees C. Whole heads were placed into 20% sucrose overnight and embedded in OCT. Mouse heads were sectioned at 12 um increments using a cryostat and sections mounted on glass slides. Sections were blocked in 3% bovine serum albumin (BSA) + 0.05% Triton-X for 1 h at room temperature and incubated with primary antibodies at a dilution of 1:100. Following incubation with primary antibody(s), sections were incubated with appropriate Alexa Fluor-conjugated secondary antibodies and DAPI (Invitrogen, Carlsbad, CA, United States). In situ hybridization was completed using the ACD Bio Multiplex Fluorescent Detection assay kit (Neward, CA) and their probes against Sox2 and Sox2ot., , # Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2

[https://doi.org/10.5061/dryad.41ns1rnr6](https://doi.org/10.5061/dryad.41ns1rnr6)

## Description of the data and file structure

Images are czi, tiff, or jpeg extension and can be opened using ImageJ/Fiji. For czi, use the Bio-Formats plugin.

**Figure 3**: In the subfolder \"RNAscope\" there are raw czi files for the samples Control, Control +RA (retinoic acid) treatment, Foxc1 mutant, Foxc1 mutant + RA with the RNAscope probe staining DAPI (channel 4), Sox2ot (channel 2) and Sox2 (channel 1). The corresponding single channel JPEG files are also in the folder. 

**Figure 4**: Contents in zip file contain two folders: \"Notch1 and Dll1\" and \"Sox2 and NICD\".

The \"Notch1 and Dll1\" subfolder contains individual JPEG images for Control, Control +RA treatment, Foxc1 Mutant, and Foxc1 Mutant + RA treatment for the following immunohistochemical stains: Dll1, Notch1 and merged. There are also the raw CZ...,