RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides

Abstract

Locomotor activity rhythms are controlled by a network of ~150 circadian neurons within the adult Drosophila brain. They are subdivided based on their anatomical locations and properties. We profiled transcripts “around the clock” from three key groups of circadian neurons with different functions. We also profiled a non-circadian outgroup, dopaminergic (TH) neurons. They have cycling transcripts but fewer than clock neurons as well as low expression and poor cycling of clock gene transcripts. This suggests that TH neurons do not have a canonical circadian clock and that their gene expression cycling is driven by brain systemic cues. The three circadian groups are surprisingly diverse in their cycling transcripts and overall gene expression patterns, which include known and putative novel neuropeptides. Even the overall phase distributions of cycling transcripts are distinct, indicating that different regulatory principles govern transcript oscillations. This surprising cell-type diversity parallels the functional heterogeneity of the different neurons.

Allatostatin-C/AstC-R2 Is a Novel Pathway to Modulate the Circadian Activity Pattern in Drosophila

“…To characterize gene expression within subpopulations of the Drosophila circadian neural network, our lab previously conducted mRNA profiling on the LNvs, LNds, and a subset of the DN1ps (Figure 1 A ), and we focused on neuropeptide transcripts [15]. The sequencing data indicated high levels of the Allatostatin-C ( AstC ) transcript in DN1ps, whereas there are lower levels in the LNds (three times lower; p < 0.0001) and no detectable AstC transcript in the LNvs (Figure 1 B ).…”

“…To identify additional circadian neuropeptides, we exploited RNA-seq data generated from purified LNvs, LNds, and DN1ps to identify known neuropeptide transcripts that are strongly expressed in circadian neurons [15]. We prioritized the DN1p cluster for the possibility of identifying additional neuropeptides, especially within those neurons with uncharacterized signaling mechanisms.…”

“…We prioritized the DN1p cluster for the possibility of identifying additional neuropeptides, especially within those neurons with uncharacterized signaling mechanisms. Allatostatin-C (AstC) transcripts were highly expressed in the DN1ps and found at much lower levels in the LNvs and the LNds [15]. Intriguingly, transcripts encoding the AstC receptor 2 (AstC-R2) were also detected in the LNds [15].…”

“…Allatostatin-C (AstC) transcripts were highly expressed in the DN1ps and found at much lower levels in the LNvs and the LNds [15]. Intriguingly, transcripts encoding the AstC receptor 2 (AstC-R2) were also detected in the LNds [15]. Thus, we predicted that AstC/AstC-R2 would be a novel intra-clock signaling pathway.…”

A 50-Year Personal Journey: Location, Gene Expression, and Circadian Rhythms

“…Most fly neurons may therefore be "clockless," of which a specific example is the dopaminergic system. Most of these neurons seem to be missing clock gene expression (Abruzzi et al 2017); mammalian dopaminergic neurons also may not express clock gene transcripts (S Nelson, pers. comm.).…”