NPAS4 regulates the transcriptional response of suprachiasmatic nucleus neurons to photic input

In mammals, the hypothalamic suprachiasmatic nucleus (SCN) is the master circadian pacemaker. It is primarily entrained by environmental photic stimuli. However, the molecular bases of the response of heterogeneous cells in the SCN to photic stimuli is not fully understood. In this study, we combined bulk RNA/ChIP/single nuclei sequencing with circadian behavioral assays to investigate cellular identities in the SCN and explore how they react to photic stimuli. We identified 3 major peptidergic cells in the SCN, Avp-expressing, Vip-expressing and Cck-expressing cells. In each peptidergic cell type, there is a light responsive cell cluster, and each of these is enriched for Neuronal PAS Domain Protein 4 (NPAS4) target genes. In addition, Npas4 null mice have a 1hr longer circadian period in constant darkness and a damped phase responsive curve to photic stimuli. Bulk RNA seq in Npas4-/- SCN revealed a reduced magnitude of light induced gene expression. Together, our data indicate that NPAS4 is part of the machinery that orchestrates the molecular response to photic stimuli in the SCN. Overall design: 1) Bulk RNA seq for light stimulation in wildtype mice: 2-4 replicates are involved in each condition. There are two dark control conditions, one is from CT17, the beginning of the light pulse and the other is from CT23, the end of the light pulse. In addition, there are 4 light pulse conditions, 0.5, 1, 3, and 6 hrs in length of light simulation. Each replicate contains 6 pairs of SCNs. 2) Bulk RNA seq for light stimulation in Npas4 null mice and control wild type littermates: 3 replicates are involved in each condition. There are 4 conditions total: wildtype with and without 1 hr light pulse at CT17 and Npas4-/- mice with and without 1 hr light pulse at CT17. Each replicate contains 6 pairs of SCNs. 3) ChIPseq: Two samples, each containing 2 pairs of SCN collected with or without 1 hr light stimulation. 4) Single nuclei sequencing: In total, 10 samples were analyzed. The first batch contains one dark control and one 1 hr light stimulation condition and sequencing was done by Illumina Hiseq. The second batch contains four dark control replicates and four 1 hr light stimulation replicates and sequencing was performed twice by Illumina NovaSeq.