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

Abstract

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.

A neurotransmitter atlas ofC. elegansmales and hermaphrodites

“… (A) Dim expression of eat-4(syb4257) in head neurons ASK and ADL is consistent with previous fosmid-based reporter expression. RIC expression is consistent with previous observation using the same reporter allele (R eilly et al . 2022).…”

Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity

“…This is based on our finding that the loss of a single HDTF (Bsh) results in reduced lamina neuron diversity (only L1-3), which may represent a simpler ancestral brain. A similar observation was described in C. elegans where the loss of a single terminal selector caused two different neuron types to become identical, which was speculated to be the ancestral ground state (Arlotta and Hobert, 2015; Cros and Hobert, 2022; Reilly et al, 2022), suggesting phylogenetically conserved principles observed in highly distinct species. An interesting possibility is that evolutionarily primitive insects, such as silverfish (Truman and Riddiford, 1999), lack Bsh expression and L4/L5 neurons, retaining only the core motion detection L1-L3 neurons.…”

“…Terminal selector HDTFs not only drive the expression of neuron functional identity genes but also activate pan-neuronal genes (Hobert, 2021; Howell et al, 2015; Kratsios et al, 2015; Stefanakis et al, 2015). Loss of terminal selector HDTFs frequently results in altered neuronal identity and function (Arlotta and Hobert, 2015; Cros and Hobert, 2022; Reilly et al, 2022).…”

Notch signaling and Bsh homeodomain activity are integrated to diversifyDrosophilalamina neuron types

“…While most TTFs are not maintained in neurons, their function is likely maintained by another TF, e.g., HDTF, which is persistently expressed in neurons. Indeed, HDTFs function as terminal selectors and control the expression of neuronal identity genes (Cros and Hobert, 2022;Hobert, 2021;Howell et al, 2015;Reilly et al, 2022Reilly et al, , 2020. The primary HDTF Bsh specifies L4 and L5 neuronal fates (Xu et al, 2023).…”