Suprachiasmatic VIP neurons are required for normal circadian rhythmicity with a subset expressing a molecularly distinct pacemaker profile

The hypothalamic suprachiasmatic (SCN) clock contains several neurochemically defined cell groups that contribute to the genesis of circadian rhythms. Using cell specific and genetically-targeted approaches we have confirmed an indispensable role for vasoactive intestinal polypeptide expressing SCN (SCNVIP) neurons in generating the mammalian locomotor activity (LMA) circadian rhythm. Optogenetic-assisted circuit mapping revealed functional, di-synaptic connectivity between SCNVIP neurons and dorsomedial hypothalamic neurons, providing a circuit substrate by which SCNVIP neurons may regulate LMA rhythms. In vivo photometry revealed that while SCNVIP neurons are acutely responsive to light, their activity is otherwise behavioral state invariant. Single-nuclei RNA-sequencing revealed SCNVIP neurons comprise two transcriptionally distinct subtypes, including putative pacemaker and non-pacemaker populations. Given that SCNVIP neurons constitute ~10% of the total SCN population, and that other cell groups were unable to sustain coherent circadian LMA rhythms following SCNVIP disruption, our findings demonstrate a disproportionately large influence of the SCNVIP cell population on pacemaker function. Single-nuclei RNA-Seq (sNuc-Seq) analysis of 190 single-nuclei samples and 2 10-nuclei samples from SCN tissue of two 6wk old mice (pooled tissue) and one 10wk old mouse