Astrocytes and neurons share brain region-specific transcriptional signatures (RNAseq: NeuronsP0)

Neuronal cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterised by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and glia. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis reveals the existence of common nucleus-specific progenitors for neurons and glia. Consistent with their shared molecular signature, regional specificity is maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair. Thalamic neurons were isolated by FACS based on fluorescence intensity of dual genetic labelling by Gbx2CreER-IRES-EGFP/+::R26lsl-tdTomato/+. Transcriptomic analysis was made on total RNA from 3 different populations of Thalamic nuclei (dorsolateral Geniculate Nucleus (dLGN), Medial Geniculate Nucleus, ventral division (MGv) and Ventral Posteriomedial Nucleus(VPM) at Post-natal day 0 (P0). In overall, 11 samples replicates were analyzed from thalamic primary sensory nuclei (4 from dLGN, 3 from MGV and 4 from VPM).