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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE305355 | GEO | 2025/11/15

REPOSITORIES: GEO

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Control of ciliary transcriptional programs during spermatogenesis by antagonistic transcription factors

Project description:Cilia and flagella are dynamicallyregulatedduring development and differentiation. Coordination of temporal and spatial transcription regulators are essential for ciliogenesis. We here report that XAP5 and XAP5L are two conserved pairs of antagonistic transcription regulators that control ciliary transcriptional programs during spermatogenesis. Male mice lacking either XAP5 or XAP5L display infertility, as a result of meiotic prophase arrest and sperm cilia malformation, respectively. XAP5 positively regulates the ciliary gene expression by activating the key regulators including FOXJ1 and RFX families during the early stage of spermatogenesis. In contrast, XAP5L negatively regulates the expression of ciliary genes via repressing these ciliary transcription factors during the spermiogenesis stage. Taken together, our data provide new insights into the mechanisms by which temporal and spatial transcription regulators are coordinated to control ciliary transcriptional programs during spermatogenesis.

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Genome-wide mapping of Xap5 and Nono binding sites by CUT&Tag in NIH/3T3 cells

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Coordinated genomic control of ciliogenesis and cell movement by Rfx2

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Coordinated genomic control of ciliogenesis and cell movement by Rfx2

Project description:We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of Rfx2-regulated transcripts and chromosomal binding sites, we provide a comprehensive accounting of the target genes by which Rfx2 controls ciliogenesis and cilia beating in vertebrates. RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control

2013-12-12 | E-GEOD-50593 | biostudies-arrayexpress

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

Project description:Cilia are ubiquitous cell surface projections that modulate various sensory- and motility based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. As new components required for cilium biogenesis and function remain unidentified, we sought to further define and validate the transcriptional targets of the ciliogenic C. elegans RFX transcription factor DAF-19. To this end, transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using selectively staged embryos where ciliogenesis occurs in most ciliated sensory neurons (CSNs). Statistical comparisons between the two populations revealed 881 differentially regulated genes with 1.5-fold change or greater. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional-GFP fusions revealed CSN-specific expression patterns for 9 of 12 candidate genes. We show that two uncharacterized candidate genes, which we term dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and interestingly, is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK-7/CCRK-related serine-threonine kinase that is necessary for the proper function of intraflagellar transport (IFT), a process critical for cilium biogenesis. Together, our comparative microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover—in addition to DYF-17 and DYF-18—cellular components important for cilium formation and function. 4 daf-19,daf12; 4 daf-12; 4 WT

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2018-08-05 | GSE60538 | GEO

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

2011-07-26 | GSE25633 | GEO

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