Identification of candidate ciliary microtubule-associated proteins using CEP41 proximity labeling

Primary cilia are microtubule-based signaling organelles whose dysfunction results in a wide spectrum of ciliopathies. Extensive studies have established the functional and clinical importance of ciliary microtubule associated proteins (ciliary MAPs), but the repertoire of specialized ciliary MAPs remains incompletely defined. Here, we used the ciliopathy-associated MAP CEP41 as a BioID bait to probe proteins proximal to ciliary microtubules. Quantitative proteomics and cilia-focused prioritization identified a ciliary MAP-enriched protein set, revealed a poorly characterized Septin-9 isoform, and supported C7orf57/FCAP33, CCDC34, and PSRC1 as novel ciliary MAPs. CCDC34 and PSRC1 did not affect cilia architecture or ciliation, indicating roles in structure-independent ciliary functions, whereas C7orf57 overexpression increased cilium length. Microtubule association analysis reveals C7orf57 as a paclitaxel sensitive MAP that associates with microtubule through its N-terminal regions. Together, these findings expand the ciliary MAP repertoire and provide a resource for prioritizing candidates for future studies of cilia biology and ciliopathies.