The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34

An enteric neuron-expressed variant ionotropic receptor detects ingested salts to regulate salt stress resistance

The detection of internal chemicals by interoceptive chemosensory pathways is critical for regulating metabolism and physiology. The molecular identities of interoceptors, and the functional consequences of chemosensation by specific interoceptive neurons remain to be fully described. The C. elegans pharyngeal neuronal network is anatomically and functionally homologous to the mammalian enteric nervous system. Here, we show that the I3 pharyngeal enteric neuron responds to cations via an I3-specific variant ionotropic receptor (IR) to regulate salt stress tolerance. The GLR-9 IR, located at the gut lumen-exposed sensory end of I3, is necessary and sufficient for salt sensation, establishing a chemosensory function for IRs beyond insects. Salt detection by I3 protects specifically against high salt stress, as glr-9 mutants show reduced tolerance of hypertonic salt but not sugar solutions, with or without prior acclimation. While cholinergic signaling from I3 promotes tolerance to acute high salt stress, peptidergic signaling from I3 during acclimation is essential for resistance to a subsequent high salt challenge. Transcriptomic analyses show that I3 regulates salt tolerance in part via regulating the expression of osmotic stress response genes in distal tissues. Our results describe the mechanisms by which chemosensation mediated by a defined enteric neuron regulates physiological homeostasis in response to a specific abiotic stress.

Protocol to identify transcription factor target genes using TargetOrtho2

TargetOrtho2 uses transcription factor binding site information to predict transcription factor targets in C. elegans, based on an in silico phylogenetic footprinting approach. Here, we present a protocol to identify transcription factor target genes using a new version of TargetOrtho2. We provide instructions for installing TargetOrtho2 and its required suite of programs, for predicting transcription factor target genes, and for updating and adding new genomes to TargetOrtho2.

Nervous system-wide analysis of all C. elegans cadherins reveals neuron-specific functions across multiple anatomical scales

Differential expression of cell adhesion proteins is a hallmark of cell-type diversity across the animal kingdom. Gene family-wide characterization of their organismal expression and function is, however, lacking. Using genome-engineered reporter alleles, we established an atlas of expression of the entire set of 12 cadherin gene family members in the nematode Caenorhabditis elegans, revealing differential expression across neuronal classes, a dichotomy between broadly and narrowly expressed cadherins, and several context-dependent temporal transitions in expression across development. Engineered mutant null alleles of cadherins were analyzed for defects in morphology, behavior, neuronal soma positions, neurite neighborhood topology and fasciculation, and localization of synapses in many parts of the nervous system. This analysis revealed a restricted pattern of neuronal differentiation defects at discrete subsets of anatomical scales, including a novel role of cadherins in experience-dependent electrical synapse formation. In total, our analysis results in previously little explored perspectives on cadherin deployment and function.

Synergistic Co-Cu Dual-Atom Nanozyme with Promoted Catalase-like Activity for Parkinson's Disease Treatment

Neurodegenerative diseases like Parkinson's disease (PD) are intimately associated with oxidative stress due to the excessive highly reactive oxygen species (ROS), leading to the damage of dopaminergic neurons. Herein, we develop a Co-Cu dual-atom nanozyme (CoCu-DAzyme) by uniformly anchoring Co and Cu active sites onto an AlO(OH) substrate that exhibits remarkable catalase-like catalytic activity, far exceeding that of the Co or Cu single-atom counterparts. The following density functional theory calculations reveal that the Co sites efficiently enable H2O2 adsorption, while Cu sites promote charge transfer, synergistically promoting the catalytic decomposition of H2O2 into H2O and O2. Encouragingly, the developed CoCu-DAzyme notably ameliorates α-synuclein aggregation and alleviates the motor dysfunction inCaenorhabditis elegansPD models by substantively scavenging in vivo ROS. This research shows a novel therapeutic strategy for oxidative-stress-related neurodegenerative disorders by developing well-engineered nanozymes.

Almost 40 years of studying homeobox genes in C. elegans

Homeobox genes are among the most deeply conserved families of transcription factor-encoding genes. Following their discovery in Drosophila, homeobox genes arrived on the Caenorhabditis elegans stage with a vengeance. Between 1988 and 1990, just a few years after their initial discovery in flies and vertebrates, positional cloning and sequence-based searches showed that C. elegans contains HOX cluster genes, an apparent surprise given the simplicity and non-segmented body plan of the nematode, as well as many other non-clustered homeobox genes of all major subfamilies (e.g. LIM, POU, etc.). Not quite 40 years later, we have an exceptionally deep understanding of homeodomain protein expression and function in C. elegans, revealing their prevalent role in nervous system development. In this Spotlight, we provide a historical perspective and a non-comprehensive journey through the C. elegans homeobox field and discuss open questions and future directions.

Ageing, proteostasis, and the gut: Insights into neurological health and disease

Recent research has illuminated the profound bidirectional communication between the gastrointestinal tract and the brain, furthering our understanding of neurological ailments facilitating possible therapeutic strategies. Technological advancements in high-throughput sequencing and multi-omics have unveiled significant alterations in gut microbiota and their metabolites in various neurological disorders. This review provides a thorough analysis of the role of microbiome-gut-brain axis in neurodegenerative disease pathology, linking it to reduced age-associated proteostasis. We discuss evidences that substantiate the existence of a gut-brain cross talk ranging from early clinical accounts of James Parkinson to Braak's hypothesis. In addition to understanding of microbes, the review particularly entails specific metabolites which are altered in neurodegenerative diseases. The regulatory effects of microbial metabolites on protein clearance mechanisms, proposing their potential therapeutic implications, are also discussed. By integrating this information, we advocate for a combinatory therapeutic strategy that targets early intervention, aiming to restore proteostasis and ameliorate disease progression. This approach not only provides a new perspective on the pathogenesis of neurodegenerative diseases but also highlights innovative strategies to combat the increasing burden of these age-related disorders.

A neurotransmitter atlas of C. elegans males and hermaphrodites

Mapping neurotransmitter identities to neurons is key to understanding information flow in a nervous system. It also provides valuable entry points for studying the development and plasticity of neuronal identity features. In the Caenorhabditis elegans nervous system, neurotransmitter identities have been largely assigned by expression pattern analysis of neurotransmitter pathway genes that encode neurotransmitter biosynthetic enzymes or transporters. However, many of these assignments have relied on multicopy reporter transgenes that may lack relevant cis-regulatory information and therefore may not provide an accurate picture of neurotransmitter usage. We analyzed the expression patterns of 16 CRISPR/Cas9-engineered knock-in reporter strains for all main types of neurotransmitters in C. elegans (glutamate, acetylcholine, GABA, serotonin, dopamine, tyramine, and octopamine) in both the hermaphrodite and the male. Our analysis reveals novel sites of expression of these neurotransmitter systems within both neurons and glia, as well as non-neural cells, most notably in gonadal cells. The resulting expression atlas defines neurons that may be exclusively neuropeptidergic, substantially expands the repertoire of neurons capable of co-transmitting multiple neurotransmitters, and identifies novel sites of monoaminergic neurotransmitter uptake. Furthermore, we also observed unusual co-expression patterns of monoaminergic synthesis pathway genes, suggesting the existence of novel monoaminergic transmitters. Our analysis results in what constitutes the most extensive whole-animal-wide map of neurotransmitter usage to date, paving the way for a better understanding of neuronal communication and neuronal identity specification in C. elegans.

Compressed sensing based approach identifies modular neural circuitry driving learned pathogen avoidance

An animal's survival hinges on its ability to integrate past information to modify future behavior. The nematode C. elegans adapts its behavior based on prior experiences with pathogen exposure, transitioning from attraction to avoidance of the pathogen. A systematic screen for the neural circuits that integrate the information of previous pathogen exposure to modify behavior has not been feasible because of the lack of tools for neuron type specific perturbations. We overcame this challenge using methods based on compressed sensing to efficiently determine the roles of individual neuron types in learned avoidance behavior. Our screen revealed that distinct sets of neurons drive exit from lawns of pathogenic bacteria and prevent lawn re-entry. Using calcium imaging of freely behaving animals and optogenetic perturbations, we determined the neural dynamics that regulate one key behavioral transition after infection: stalled re-entry into bacterial lawns. We find that key neuron types govern pathogen lawn specific stalling but allow the animal to enter nonpathogenic E. coli lawns. Our study shows that learned pathogen avoidance requires coordinated transitions in discrete neural circuits and reveals the modular structure of this complex adaptive behavioral response to infection.

Neurogenesis in Caenorhabditis elegans

Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies and functions of neurons. Neuronal cells share multiple structural and physiological features, but they also come in a large diversity of types or classes that give the nervous system its broad range of functions and plasticity. This diversity, first recognized over a century ago, spurred classification efforts based on morphology, function, and molecular criteria. Caenorhabditis elegans, with its precisely mapped nervous system at the anatomical level, an extensive molecular description of most of its neurons, and its genetic amenability, has been a prime model for understanding how neurons develop and diversify at a mechanistic level. Here, we review the gene regulatory mechanisms driving neurogenesis and the diversification of neuron classes and subclasses in C. elegans. We discuss our current understanding of the specification of neuronal progenitors and their differentiation in terms of the transcription factors involved and ensuing changes in gene expression and chromatin landscape. The central theme that has emerged is that the identity of a neuron is defined by modules of gene batteries that are under control of parallel yet interconnected regulatory mechanisms. We focus on how, to achieve these terminal identities, cells integrate information along their developmental lineages. Moreover, we discuss how neurons are diversified postembryonically in a time-, genetic sex-, and activity-dependent manner. Finally, we discuss how the understanding of neuronal development can provide insights into the evolution of neuronal diversity.

Adaptive Cellular Radiations and the Genetic Mechanisms Underlying Animal Nervous System Diversification

In animals, the nervous system evolved as the primary interface between multicellular organisms and the environment. As organisms became larger and more complex, the primary functions of the nervous system expanded to include the modulation and coordination of individual responsive cells via paracrine and synaptic functions as well as to monitor and maintain the organism's own internal environment. This was initially accomplished via paracrine signaling and eventually through the assembly of multicell circuits in some lineages. Cells with similar functions and centralized nervous systems have independently arisen in several lineages. We highlight the molecular mechanisms that underlie parallel diversifications of the nervous system.

SIX4 Activation in Inflammatory Response Drives the Transformation of Colorectal Epithelium into Inflammation and Tumor via Feedback-Enhancing Inflammatory Signaling to Induce Tumor Stemness Signaling

Some colorectal cancer patients have experienced normal epithelial transformation into inflammatory and tumor states, but the molecular basis still needs to be further determined. The expression levels of SIX4 are gradually increased in dextran sodium sulfate (DSS) and azoxymethane (AOM)/DSS-induced colonic epithelial inflammation and tumors, respectively, in mice. Targeting SIX4 alleviates intestinal inflammation occurrence and reduces adenoma formation in mice. Clinical sample assays indicated that SIX4 is upregulated in inflammatory bowel disease (IBD) and colorectal cancer (CRC) tissues compared to normal colorectal tissues. In a subsequent study, we found that SIX4, transcriptionally activated by the proinflammatory IL-6/STAT3 signal, binds to c-Jun to transcribe IL-6, thus forming a positive IL-6/STAT3/SIX4/c-Jun feedback loop, which further induces intestinal inflammation occurrence. In addition, elevated SIX4 also induces the expression of DeltaNp63, rather than wild-type p63, by binding to its promoter and thus facilitates the activation of tumor stemness signals, which ultimately leads to the formation of colorectal cancer. Our study first observes that activated SIX4 in inflammation induction drives the transformation of colorectal epithelium into inflammation and tumor, which demonstrates SIX4 as a significant therapeutic target in IBD and colitis-associated colorectal cancer (CAC) and CRC pathogenesis.

A neurotransmitter atlas of C. elegans males and hermaphrodites

Mapping neurotransmitter identities to neurons is key to understanding information flow in a nervous system. It also provides valuable entry points for studying the development and plasticity of neuronal identity features. In the C. elegans nervous system, neurotransmitter identities have been largely assigned by expression pattern analysis of neurotransmitter pathway genes that encode neurotransmitter biosynthetic enzymes or transporters. However, many of these assignments have relied on multicopy reporter transgenes that may lack relevant cis-regulatory information and therefore may not provide an accurate picture of neurotransmitter usage. We analyzed the expression patterns of 16 CRISPR/Cas9-engineered knock-in reporter strains for all main types of neurotransmitters in C. elegans (glutamate, acetylcholine, GABA, serotonin, dopamine, tyramine, and octopamine) in both the hermaphrodite and the male. Our analysis reveals novel sites of expression of these neurotransmitter systems within both neurons and glia, as well as non-neural cells. The resulting expression atlas defines neurons that may be exclusively neuropeptidergic, substantially expands the repertoire of neurons capable of co-transmitting multiple neurotransmitters, and identifies novel neurons that uptake monoaminergic neurotransmitters. Furthermore, we also observed unusual co-expression patterns of monoaminergic synthesis pathway genes, suggesting the existence of novel monoaminergic transmitters. Our analysis results in what constitutes the most extensive whole-animal-wide map of neurotransmitter usage to date, paving the way for a better understanding of neuronal communication and neuronal identity specification in C. elegans.

Spatiotemporal analysis of mRNA-protein relationships enhances transcriptome-based developmental inference

Elucidating the complex relationships between mRNA and protein expression at high spatiotemporal resolution is critical for unraveling multilevel gene regulation and enhancing mRNA-based developmental analyses. In this study, we conduct a single-cell analysis of mRNA and protein expression of transcription factors throughout C. elegans embryogenesis. Initially, cellular co-presence of mRNA and protein is low, increasing to a medium-high level (73%) upon factoring in delayed protein synthesis and long-term protein persistence. These factors substantially affect mRNA-protein concordance, leading to potential inaccuracies in mRNA-reliant gene detection and specificity characterization. Building on the learned relationship, we infer protein presence from mRNA expression and demonstrate its utility in identifying tissue-specific genes and elucidating relationships between genes and cells. This approach facilitates identifying the role of sptf-1/SP7 in neuronal lineage development. Collectively, this study provides insights into gene expression dynamics during rapid embryogenesis and approaches for improving the efficacy of transcriptome-based developmental analyses.

Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs

In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.

A protocol to transform a fluorescent reporter from a nuclear to a cytoplasmic location

To facilitate cell identification for expression pattern analysis in C. elegans , an SL2::GFP::H2B fluorescent reporter cassette has become a popular and widely used choice to generate nuclear localized reporter alleles by CRISPR/Cas9 genome engineering. When added at the 3' end of a locus of interest, this cassette concentrates GFP into the nucleus and permits the identification of expressing cells, for example with the help of the NeuroPAL tool. However, there are instances in which it is desirable to visualize the complete morphology of a cell that expresses an SL2::GFP::H2B reporter cassette. We describe here a CRISPR/Cas9-engineering strategy to transform an endogenous SL2::GFP::H2B tag into a cytosolic tag by insertion of the self-cleaving T2A tag in between GFP and H2B.

Toolkits for detailed and high-throughput interrogation of synapses in C. elegans

Visualizing synaptic connectivity has traditionally relied on time-consuming electron microscopy-based imaging approaches. To scale the analysis of synaptic connectivity, fluorescent protein-based techniques have been established, ranging from the labeling of specific pre- or post-synaptic components of chemical or electrical synapses to transsynaptic proximity labeling technology such as GRASP and iBLINC. In this paper, we describe WormPsyQi, a generalizable image analysis pipeline that automatically quantifies synaptically localized fluorescent signals in a high-throughput and robust manner, with reduced human bias. We also present a resource of 30 transgenic strains that label chemical or electrical synapses throughout the nervous system of the nematode Caenorhabditis elegans, using CLA-1, RAB-3, GRASP (chemical synapses), or innexin (electrical synapse) reporters. We show that WormPsyQi captures synaptic structures in spite of substantial heterogeneity in neurite morphology, fluorescence signal, and imaging parameters. We use these toolkits to quantify multiple obvious and subtle features of synapses - such as number, size, intensity, and spatial distribution of synapses - in datasets spanning various regions of the nervous system, developmental stages, and sexes. Although the pipeline is described in the context of synapses, it may be utilized for other 'punctate' signals, such as fluorescently tagged neurotransmitter receptors and cell adhesion molecules, as well as proteins in other subcellular contexts. By overcoming constraints on time, sample size, cell morphology, and phenotypic space, this work represents a powerful resource for further analysis of synapse biology in C. elegans.

Mechanisms of lineage specification in Caenorhabditis elegans

The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.

The neuropeptidergic connectome of C. elegans

Efforts are ongoing to map synaptic wiring diagrams, or connectomes, to understand the neural basis of brain function. However, chemical synapses represent only one type of functionally important neuronal connection; in particular, extrasynaptic, "wireless" signaling by neuropeptides is widespread and plays essential roles in all nervous systems. By integrating single-cell anatomical and gene-expression datasets with biochemical analysis of receptor-ligand interactions, we have generated a draft connectome of neuropeptide signaling in the C. elegans nervous system. This network is characterized by high connection density, extended signaling cascades, autocrine foci, and a decentralized topology, with a large, highly interconnected core containing three constituent communities sharing similar patterns of input connectivity. Intriguingly, several key network hubs are little-studied neurons that appear specialized for peptidergic neuromodulation. We anticipate that the C. elegans neuropeptidergic connectome will serve as a prototype to understand how networks of neuromodulatory signaling are organized.

Ancestral glycoprotein hormone-receptor pathway controls growth in C. elegans

In vertebrates, thyrostimulin is a highly conserved glycoprotein hormone that, besides thyroid stimulating hormone (TSH), is a potent ligand of the TSH receptor. Thyrostimulin is considered the most ancestral glycoprotein hormone and orthologs of its subunits, GPA2 and GPB5, are widely conserved across vertebrate and invertebrate animals. Unlike TSH, however, the functions of the thyrostimulin neuroendocrine system remain largely unexplored. Here, we identify a functional thyrostimulin-like signaling system in Caenorhabditis elegans. We show that orthologs of GPA2 and GPB5, together with thyrotropin-releasing hormone (TRH) related neuropeptides, constitute a neuroendocrine pathway that promotes growth in C. elegans. GPA2/GPB5 signaling is required for normal body size and acts through activation of the glycoprotein hormone receptor ortholog FSHR-1. C. elegans GPA2 and GPB5 increase cAMP signaling by FSHR-1 in vitro. Both subunits are expressed in enteric neurons and promote growth by signaling to their receptor in glial cells and the intestine. Impaired GPA2/GPB5 signaling causes bloating of the intestinal lumen. In addition, mutants lacking thyrostimulin-like signaling show an increased defecation cycle period. Our study suggests that the thyrostimulin GPA2/GPB5 pathway is an ancient enteric neuroendocrine system that regulates intestinal function in ecdysozoans, and may ancestrally have been involved in the control of organismal growth.

Neuronal contact predicts connectivity in the C. elegans brain

Axons must project to particular brain regions, contact adjacent neurons, and choose appropriate synaptic targets to form a nervous system. Multiple mechanisms have been proposed to explain synaptic partnership choice. In a "lock-and-key" mechanism, first proposed by Sperry's chemoaffinity model,¹ a neuron selectively chooses a synaptic partner among several different, adjacent target cells, based on a specific molecular recognition code.² Alternatively, Peters' rule posits that neurons indiscriminately form connections with other neuron types in their proximity; hence, neighborhood choice, determined by initial neuronal process outgrowth and position, is the main predictor of connectivity.^3,4 However, whether Peters' rule plays an important role in synaptic wiring remains unresolved.⁵ To assess the nanoscale relationship between neuronal adjacency and connectivity, we evaluate the expansive set of C. elegans connectomes. We find that synaptic specificity can be accurately modeled as a process mediated by a neurite adjacency threshold and brain strata, offering strong support for Peters' rule as an organizational principle of C. elegans brain wiring.

Dscam1 overexpression impairs the function of the gut nervous system in Drosophila

BACKGROUND

Down syndrome (DS) patients have a 100-fold increase in the risk of Hirschsprung syndrome of the colon and rectum (HSCR), a lack of enteric neurons in the colon. The leading DS candidate gene is trisomy of the Down syndrome cell adhesion molecule (DSCAM).

RESULTS

We find that Dscam1 protein is expressed in the Drosophila enteric/stomatogastric nervous system (SNS). Axonal Dscam1 phenotypes can be rescued equally by diverse isoforms. Overexpression of Dscam1 resulted in frontal and hindgut nerve overgrowth. Expression of dominant negative Dscam1-ΔC led to a truncated frontal nerve and increased branching of the hindgut nerve. Larval locomotion is influenced by feeding state, and we found that the average speed of larvae with Dscam1 SNS expression was reduced, whereas overexpression of Dscam1-ΔC significantly increased the speed. Dscam1 overexpression reduced the efficiency of food clearance from the larval gut.

CONCLUSION

Our work demonstrates that overexpression of Dscam1 can perturb gut function in a model system.

The lower Cambrian lobopodian Cardiodictyon resolves the origin of euarthropod brains

For more than a century, the origin and evolution of the arthropod head and brain have eluded a unifying rationale reconciling divergent morphologies and phylogenetic relationships. Here, clarification is provided by the fossilized nervous system of the lower Cambrian lobopodian Cardiodictyon catenulum, which reveals an unsegmented head and brain comprising three cephalic domains, distinct from the metameric ventral nervous system serving its appendicular trunk. Each domain aligns with one of three components of the foregut and with a pair of head appendages. Morphological correspondences with stem group arthropods and alignments of homologous gene expression patterns with those of extant panarthropods demonstrate that cephalic domains of C. catenulum predate the evolution of the euarthropod head yet correspond to neuromeres defining brains of living chelicerates and mandibulates.

Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification

Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 14 homeobox genes in 24 distinct neuron classes that are mostly unrelated by location, function and lineage history. 12 of these 24 neuron classes had no homeobox gene function ascribed to them before, while in the other 12 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analyses, 113 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.