Single cell RNA-seq of the developing mouse hypothalamus

Neurons in the hypothalamic arcuate nucleus (ARC) are fundamental regulators of energy homeostasis, growth and reproduction. Spatially overlapping subpopulations of ARC neurons produce specific neuropeptides including melanocortins, opioids, neuropeptide Y, growth hormone releasing hormone and kisspeptin. However, the developmental pathways controlling ARC neuron specification, differentiation and maturation remain poorly understood relative to more structurally ordered brain regions. Here, we analyzed the transcriptomes of individual mouse ARC neurons sorted for expression of a Proopiomelanocortin-Td-dsRed transgene at four embryonic (E11.5, E13.5, E15.5 and E17.5) and two postnatal (P5 and P12) ages. There was an unanticipated complexity of neurochemical subpopulations in the developing ARC characterized by low, medium or high levels of Pomc transcripts and distinct temporal patterns of transcription factor expression. Moreover, sizeable fractions of Pomc-positive neural progenitors differentiated into non-POMC neurons by P12. We conclude that ARC neuronal development is highly dynamic with plasticity that may be susceptible to environmental programming. Overall design: Embryonic hypothalami were dissected at E11.5, E13.5, E15.5, and E17.5. Postnatal hypothalami were isolated from pups at postnatal day 6 (P6) and P12. In each dissection, hypothalami from at least 6 pups were pooled together to acquire enough cells for fluorescence-activated cell sorting (FACS). After FACS, cells were counted and subjected to scRNA-seq library preparation and sequencing (10x Genomics).