Transcriptomics of independent CRISPR-edited cell lines reveal ciliary-specific ARL13B-dependent changes
- 1Genetics and Molecular Biology Graduate Program, Emory University , Atlanta, GA 30322 ,
- 2Department of Human Genetics, Emory University , Atlanta, GA 30322 ,
Abstract
Primary cilia coordinate signaling pathways that regulate tissue homeostasis and development, and defects in cilia contribute to numerous ciliopathies. However, the transcriptional consequences of disrupting ciliary protein localization remain poorly defined. ARL13B is a cilia-enriched regulatory GTPase required for ciliary trafficking and signaling. The ARL13BV358A variant is undetectable in cilia yet retains known biochemical functions, providing a unique model to investigate the functions of ciliary ARL13B independently of ciliogenesis. To define transcriptional programs associated with loss of ciliary ARL13B, we generated 2 independent Arl13bV358A/V358A kidney epithelial cell lines and matched rescue lines. The ARL13BV358A mutation did not affect ciliation frequency or cilia length but altered ciliary protein composition, including loss of ARL3 and INPP5E localization and increased accumulation of TULP3. RNA sequencing revealed expression changes in genes associated with ciliary biology, mechanotransduction, epithelial organization, and kidney-related phenotypes. Despite similar ciliary phenotypes, the independently derived mutant clones displayed substantial transcriptomic heterogeneity, highlighting a potential source of variation in CRISPR-based transcriptional studies. By integrating data from the independent mutant and rescue clones, we identified a high-confidence set of 131 genes whose expression reproducibly tracked with loss and restoration of ciliary ARL13B. Together, these findings demonstrate that ciliary ARL13B is required to maintain normal ciliary composition and gene expression programs and underscore the value of multiclone, rescue-based experimental designs for robust transcriptomic analyses.
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BibTeX
@article{morrison2026transcriptomics,
title = {{Transcriptomics of independent CRISPR-edited cell lines reveal ciliary-specific ARL13B-dependent changes}},
author = {Olivia Morrison and Tamara Caspary},
journal = {G3: Genes, Genomes, Genetics},
year = {2026},
month = oct,
doi = {10.1093/g3journal/jkag292},
url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag292/8979768},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Transcriptomics of independent CRISPR-edited cell lines reveal ciliary-specific ARL13B-dependent changes
AU - Olivia Morrison
AU - Tamara Caspary
PY - 2026
DA - 2026/10/22
JO - G3: Genes, Genomes, Genetics
DO - 10.1093/g3journal/jkag292
UR - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag292/8979768
AB - Primary cilia coordinate signaling pathways that regulate tissue homeostasis and development, and defects in cilia contribute to numerous ciliopathies. However, the transcriptional consequences of disrupting ciliary protein localization remain poorly defined. ARL13B is a cilia-enriched regulatory GTPase required for ciliary trafficking and signaling. The ARL13BV358A variant is undetectable in cilia yet retains known biochemical functions, providing a unique model to investigate the functions of ciliary ARL13B independently of ciliogenesis. To define transcriptional programs associated with loss of ciliary ARL13B, we generated 2 independent Arl13bV358A/V358A kidney epithelial cell lines and matched rescue lines. The ARL13BV358A mutation did not affect ciliation frequency or cilia length but altered ciliary protein composition, including loss of ARL3 and INPP5E localization and increased accumulation of TULP3. RNA sequencing revealed expression changes in genes associated with ciliary biology, mechanotransduction, epithelial organization, and kidney-related phenotypes. Despite similar ciliary phenotypes, the independently derived mutant clones displayed substantial transcriptomic heterogeneity, highlighting a potential source of variation in CRISPR-based transcriptional studies. By integrating data from the independent mutant and rescue clones, we identified a high-confidence set of 131 genes whose expression reproducibly tracked with loss and restoration of ciliary ARL13B. Together, these findings demonstrate that ciliary ARL13B is required to maintain normal ciliary composition and gene expression programs and underscore the value of multiclone, rescue-based experimental designs for robust transcriptomic analyses.
SN - 2160-1836
ER -