An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons

Abstract

Regulatory Factor X (RFX) transcription factors (TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans, the sole RFX gene, daf-19, encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance. We sought to identify RFX/daf-19 target genes associated with neuronal functions other than ciliogenesis using comparative transcriptome analyses at different life stages of the worm. Subsequent characterization of gene expression patterns revealed one set of genes activated in the presence of DAF-19 in ciliated sensory neurons, whose activation requires the daf-19c isoform, also required for ciliogenesis. A second set of genes is downregulated in the presence of DAF-19, primarily in nonsensory neurons. The human orthologs of some of these neuronal genes are associated with human diseases. We report the novel finding that daf-19a is directly or indirectly responsible for downregulation of these neuronal genes in C. elegans by characterizing a new mutation affecting the daf-19a isoform (tm5562) and not associated with ciliogenesis, but which confers synaptic and behavioral defects. Thus, we have identified a new regulatory role for RFX TFs in the nervous system. The new daf-19 candidate target genes we have identified by transcriptomics will serve to uncover the molecular underpinnings of the pleiotropic effects that daf-19 exerts on nervous system function.

Vibration sensitivity found inCaenorhabditis elegans

“…The most likely explanation is that ciliated mechanosensory neurons are involved in frequency discrimination; however, any ciliated neurons could be involved. DAF-19 proteins are also involved in synaptic protein maintenance in non-ciliated neurons (De Stasio et al, 2018). Indeed, the shorter total distance travelled by these mutants compared with the wild-type was consistent with the abnormal roaming phenotype (Senti and Swoboda, 2008).…”

“…DAF-19A and B are expressed in non-ciliated neurons (Saito et al, 2013) and hypodermis and body wall muscle (Craig et al, 2013). Mutants defective in these gene products show abnormal dwelling and roaming behaviour (Senti and Swoboda, 2008), as a result of its role in synaptic protein maintenance (De Stasio et al, 2018). daf-19 also influences other signalling pathways, such as the innate immune response (Xie et al, 2013).…”

TheC. elegansDAF-19M module: a shift from general ciliogenesis to ciliary and behavioral specialization

“…We isolated EMS treated mutant worms using the COPAS BIOSORT (Fig 1A). From a screen of >15,000 F1 animals, we were able to isolate and maintain two mutations, both of which locate to the gene daf-19 (Fig 1B): the of3 allele locates to the dimerization domain (DIM), while the of4 allele locates to the DNA binding domain (DBD) (De Stasio et al ., 2018; Swoboda et al ., 2000; Wang et al ., 2010). Both mutations of3 and of4 cause strongly decreased klp-6 expression (Fig 1C), fluorescent dye filling defects (Fig 1E) and a dauer constitutive phenotype (Daf-c).…”

“…The C. elegans genome contains only one RFX TF gene, daf-19 ,which encodes several isoforms that govern different, yet in parts related biological functions. DAF-19A/B protein regulates synaptic homeostasis in non-ciliated neurons and DAF-19C regulates the developmental process of ciliogenesis in sensory neurons (De Stasio et al , 2018; Senti & Swoboda, 2008; Swoboda et al ., 2000). Cilia and synapses share important conceptual and anatomical parallels in connection to their biological tasks as signal transducers (Shaham, 2010).…”

DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in Pristionchus pacificus

“…First, we observed strong differences in daf‐19 function between P. pacificus and C. elegans during dauer induction. One of the most striking features found in Cel ‐ daf‐19 mutants is the Daf‐c phenotype, which is exclusively associated with the DAF‐19c isoform (De Stasio et al, ; Senti & Swoboda, ). Our analysis has revealed that none of the Ppa‐daf‐19 mutants show a Daf‐c phenotype, indicating divergence in the dauer regulatory pathway between the two species.…”