Molecular topography of an entire nervous system

Abstract

SummaryNervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of ∼23 neuropeptide-encoding genes and ∼36 neuropeptide receptors thus pointing to an expansive “wireless” signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons

“…This cell identification was done with specific landmark strains and will be reported elsewhere. It is also consistent with recent scRNA data, which revealed hlh-34 expression exclusively in AVH ( Taylor et al, 2021 ).…”

“…One potential problem of this methodology is that among a set of randomly chosen 40 neurons several neurons may not be in close enough physical proximity to potentially form synapses. To address this limitation, we utilized a recently introduced unbiased approach, termed network differential gene expression (NDGE) analysis, with an appropriate null model that takes into account membrane contact ( Taylor et al, 2021 ) to estimate the significance of unc-42 expression with synaptic linkage. This approach is a generalization of differential gene expression analysis ( Wang et al, 2019 ) that is in widespread use in single-cell RNA-sequencing literature where the gene expression differences between groups of cells are statistically tested.…”

“…Second, how does UNC-42 activate distinct target genes in distinct neuron types? Using the single cell transcriptome atlas of all C. elegans neurons ( Taylor et al, 2021 ) and a phylogenetic footprinting pipeline, described in the accompanying paper by Glenwinkel et al, we found that functionally validated UNC-42 binding sites are enriched in the cellular transcriptomes of each one of the 15 neuron classes that express UNC-42 including those genes whose expression we have shown here to be unc-42- dependent (representative examples are shown in Figure 12A ) (Glenwinkel et al, accompanying paper). This analysis strongly suggests that UNC-42 directly activates the expression of terminal gene batteries in all unc-42(+) neurons.…”

C. elegans PEZO-1 is a Mechanosensitive Ion Channel Involved in Food Sensation

“…In addition to the pharyngeal cells, we observed expression of pezo-1 in the ventral nerve cord (VNC, Figure 1D) neurons, striated muscles (Supplementary Figure 1C), coelomocytes (Supplementary Figure 1D-E), spermatheca (Supplementary Figure 1B and 1E), vulval muscles (Supplementary Figure 1F), and various male neurons including the ray neurons (Supplementary Figure 1G). Importantly, the expression pattern reported by our pezo-1 fosmid construct matches very well with the gene expression atlas for C. elegans neurons (Taylor et al ., 2020), except for the M3 neurons. The strong and varied pezo-1 expression in the pharynx along with the function of the cells expressing it, led us to investigate the potential contribution of PEZO-1 to pharyngeal function.…”

In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system

“…An expression atlas of the entire, fourth larval stage nervous system assembled through single cell transcriptomics ( Taylor et al, 2021 ; Figure 2A , Supplementary file 1B ) from which differential expression profiles were generated for each neuron class. In parallel, we used an available reporter gene atlas collectively generated by the C. elegans community over the past few decades via reporter gene analysis available at Wormbase.org ( Figure 2A , Supplementary file 1C ; Hobert et al, 2016 ).…”