Transcriptional profiling of Xap5, Nono, and Sox5 knockout mouse fibroblasts during primary ciliogenesis

The formation of primary cilia (ciliogenesis) is a fundamental process in mammalian development, governed by precise transcriptional programs. While the Rfx and Foxj1 transcription factors are known master regulators, the full scope of this control, particularly for primary cilia, is not completely understood. This study aims to define the transcriptional network downstream of the ancient, evolutionarily conserved factor Xap5, which we identified as a novel master regulator of primary ciliogenesis. To achieve this, we performed transcriptome analysis (RNA-seq) on wild-type (WT) NIH/3T3 mouse fibroblasts and derived knockout (KO) cell lines for Xap5, its interacting cofactor Nono, and a key downstream effector, Sox5. Cells were profiled following 24 hours of serum starvation, a condition that induces primary cilia formation and revealed a significant cilia elongation defect in all three knockout lines. Overall, this dataset provides a comprehensive resource for identifying the common and unique gene expression programs regulated by the Xap5-Nono-Sox5 transcriptional cascade, an Rfx-independent pathway essential for building the primary cilium. Overall design: The goal of this study was to identify the transcriptional network regulated by the Xap5-Nono-Sox5 pathway during primary ciliogenesis. To achieve this, we performed RNA-sequencing on four groups of NIH/3T3 mouse fibroblasts: Wild-type (WT), Xap5 KO, Nono KO and Sox5 KO. All cell lines were cultured and induced to form primary cilia by serum starvation for 24 hours prior to RNA extraction. The transcriptomes of the three knockout lines were then compared to the wild-type control to identify commonly and uniquely dysregulated genes, thereby defining the downstream targets of this novel ciliogenic pathway.