Robust regulatory architecture of pan-neuronal gene expression

Panneuronally expressed genes, such as genes involved in the synaptic vesicle release cycle or in neuropeptide maturation, are critical for proper function of all neurons, but the transcriptional control mechanisms that direct such genes to all neurons of a nervous system remain poorly understood in any organism. We show here that six members of the CUT superfamily of homeobox genes, which are each panneuronally expressed, control panneuronal identity specification in C. elegans. Single mutants show barely any effects on panneuronal gene expression or global nervous system function, but such effects become apparent and progressively worsen upon removal of additional CUT family members. Phenotypes of compound mutants can be rescued non-discriminately by overexpression of individual family members, indicating that gene dosage is critical for CUT gene function. Genome-wide binding profiles as well as mutation of CUT binding sites by CRISPR/Cas9 genome engineering show that CUT genes directly control the expression of panneuronal features. Lastly, we found that CUT genes act in conjunction with neuron-type specific transcription factors to control panneuronal gene expression. In conclusion, our study provides a previously missing key insight into how neuronal gene expression programs are specified and reveals a highly buffered and robust mechanism that controls the most critical functional features of all neurons. Overall design: Immunoprecipitation of neuronal nuclei at the L1 larval stage (C. elegans) in control animals as well as CUT sextuple mutant (ceh-38;ceh-44;ceh-48;ceh-41,ceh-21,ceh-39 null)