The primary cilium is an evolutionarily conserved organelle present in many eukaryotic cells, where it plays a central role in cellular signaling and environmental sensing. Despite its importance, the full set of genes required for its structure and function remains incomplete. Caenorhabditis elegans provides a powerful system to study ciliary biology due to its well-characterized nervous system and ease of genetic and experimental manipulation, enabling the identification of conserved mechanisms across species. We hypothesized that genes associated with ciliary function share expression-based features and other biological characteristics, independent of DNA sequence similarity, that can be used for their identification.

To investigate this, transcriptomic datasets were constructed from publicly available single-cell RNA sequencing data (Packer et al. 2019; Taylor et al. 2021). These datasets include neuronal cell types across developmental stages, comprising both ciliated and non-ciliated populations, and were integrated prior to analysis. Genes were filtered based on expression across different cell types and variability, and annotated ciliary genes were split into enrichment analysis and evaluation sets. Expression values were standardized, and agglomerative hierarchical clustering was applied across multiple distance thresholds. Enrichment analysis identified clusters overrepresented in ciliary genes, from which candidate genes were defined. Candidates were compared across conditions and stages, and the method was evaluated by quantifying the enrichment of evaluation-set genes within enriched clusters.

In future work, additional biological features independent of DNA sequence, such as genomic localization of functional groups and structural motifs, will be incorporated, alongside supervised machine learning approaches to improve candidate prioritization.

Co-authors: Flavio Pazos Obregón, Laura Romanelli-Cedrez, Florencia Irigoin