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X-linked retinitis pigmentosa (XLRP) is frequently caused by mutations in the retinitis pigmentosa GTPase regulator ( RPGR ) gene. A complex splicing process acts on the RPGR gene resulting in three major isoforms: RPGR ex1-19  , RPGR ORF15  and RPGR skip14/15  . We characterized the widely expressed, alternatively spliced transcript RPGR skip14/15  lacking exons 14 and 15. Using the CRISPR/eSpCas9 system, we generated HEK293T cell lines exclusively expressing the RPGR skip14/15  transcript from the endogenous RPGR gene. RPGR ex1-19  and RPGR ORF15  were knocked out. Immunocytochemistry demonstrated that the RPGR skip14/15 protein localizes along primary cilia, resembling the expression pattern of RPGR ex1-19 . The number of cilia-carrying cells was not affected by the absence of the RPGR ex1-19 and RPGR ORF15 isoforms. Co-immunoprecipitation assays demonstrated that both RPGR ex1-19 and RPGR skip14/15 interact with PDE6D, further supporting that RPGR skip14/15 is associated with the protein networks along the primary cilium. Interestingly, interaction complexes with INPP5E or RPGRIP1L were only detectable with isoform RPGR ex1-19 , but not with RPGR skip14/15 , demonstrating distinct functional properties of the major RPGR isoforms in spite of their similar subcellular localization. Our findings lead to the conclusion that protein binding sites within RPGR are mediated through alternative splicing. A tissue-specific expression ratio between RPGR skip14/15 and RPGR ex1-19 seems required to regulate the ciliary concentration of RPGR interaction partners.

The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L