Research Project: Dissecting the function and regulation of centriolar satellites: key regulators of the centrosome/ cilium complex
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Contributors
Funders
ID
EC.00089
Authors
Karalar, Elif Nur Fırat
Faculty Member
Publications
Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation
(Wiley, 2019) Gül, Şeref; Karalar, Elif Nur Fırat; Kavaklı, İbrahim Halil; Odabaşı, Ezgi; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Centriolar satellites are ubiquitous in vertebrate cells. They have recently emerged as key regulators of centrosome/cilium biogenesis, and their mutations are linked to ciliopathies. However, their precise functions and mechanisms of action remain poorly understood. Here, we generated a kidney epithelial cell line (IMCD3) lacking satellites by CRISPR/Cas9-mediated PCM1 deletion and investigated the cellular and molecular consequences of satellite loss. Cells lacking satellites still formed full-length cilia but at significantly lower numbers, with changes in the centrosomal and cellular levels of key ciliogenesis factors. Using these cells, we identified new ciliary functions of satellites such as regulation of ciliary content, Hedgehog signaling, and epithelial cell organization in three-dimensional cultures. However, other functions of satellites, namely proliferation, cell cycle progression, and centriole duplication, were unaffected in these cells. Quantitative transcriptomic and proteomic profiling revealed that loss of satellites affects transcription scarcely, but significantly alters the proteome. Importantly, the centrosome proteome mostly remains unaltered in the cells lacking satellites. Together, our findings identify centriolar satellites as regulators of efficient cilium assembly and function and provide insight into disease mechanisms of ciliopathies.
CCDC57 cooperates with microtubules and microcephaly protein CEP63 and regulates centriole duplication and mitotic progression
(Elsevier, 2020) Arslanhan, Melis Dilara; Culfa, Efraim; Gürkaşlar, Hazal Kübra; Karalar, Elif Nur Fırat; Lince Faria, Mariana; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Yes; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Centrosomes function in key cellular processes ranging from cell division to cellular signaling. Their dysfunction is linked to cancer and developmental disorders. Here, we identify CCDC57 as a pleiotropic regulator of centriole duplication, mitosis, and ciliogenesis. Combining proximity mapping with superresolution imaging, we show that CCDC57 localizes to the proximal end of centrioles and interacts with the microcephaly protein CEP63, centriolar satellite proteins, and microtubules. Loss of CCDC57 causes defects in centriole duplication and results in a failure to localize CEP63 and CEP152 to the centrosome. Additionally, CCDC57 depletion perturbs mitotic progression both in wild-type and centriole-less cells. Importantly, its centrosome-targeting region is required for its interaction with CEP63 and functions during centriole duplication and cilium assembly, whereas the microtubule-targeting region is required for its mitotic functions. Together, our results identify CCDC57 as a critical interface between centrosome and microtubule-mediated cellular processes that are deregulated in microcephaly.
Unraveling the mysteries of centriolar satellites: time to rewrite the textbooks about the centrosome/cilium complex
(American Society for Cell Biology, 2020) Batman, Umut; Karalar, Elif Nur Fırat; Odabaşı, Ezgi; N/A; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Yes; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Centriolar satellites are membraneless granules that localize and move around centrosomes and cilia. Once referred to as structures with no obvious function, research in the past decade has identified satellites as key regulators of a wide range of cellular and organismal processes. Importantly, these studies have revealed a substantial overlap between functions, proteomes, and disease links of satellites with centrosomes and cilia. Therefore, satellites are now accepted as the “third component” of the vertebrate centrosome/cilium complex, which profoundly changes the way we think about the assembly, maintenance, and remodeling of the complex at the cellular and organismal levels. In this perspective, we first provide an overview of the cellular and structural complexities of centriolar satellites. We then describe the progress in the identification of the satellite interactome, which have paved the way to a molecular understanding of their mechanism of action and assembly mechanisms. After exploring current insights into their functions as recently described by loss-of-function studies and comparative evolutionary approaches, we discuss major unanswered questions regarding their functional and compositional diversity and their functions outside centrosomes and cilia.
CCDC66 regulation of cytoskeleton and cilia stability is important for signaling and epithelial organization
(Public Library Science, 2025) Deretic, Jovana; Emek, Şeyma Cengiz; Seyrek, Ece; Karalar, Elif Nur Fırat; Emek, Şeyma Cengiz; Seyrek, Ece; Department of Molecular Biology and Genetics; School of Medicine; Yes; College of Sciences; SCHOOL OF MEDICINE
The primary cilium is a conserved, microtubule-based organelle that transduces signaling pathways essential for development and homeostasis. It dynamically assembles and disassembles in response to intrinsic and extrinsic stimuli while maintaining remarkable structural stability and tightly regulated length. The mechanisms underlying this stability and length control are not well understood. Here, we characterized CCDC66, a microtubule-associated protein linked to ciliopathies, as an important regulator of cilium maintenance and disassembly in mouse epithelial cells. Live imaging revealed that cilia in CCDC66-depleted cells frequently fluctuate in length and exhibit increased cilium disassembly and ectocytosis. Phenotypic rescue experiments and in vitro assays showed that microtubule stabilization activity of CCDC66 is required for these functions. Temporal proximity mapping identified potential new regulators and molecular pathways involved in cilium disassembly. Further characterization revealed actin cytoskeleton and vesicular trafficking as additional mechanisms by which CCDC66 may mediate its ciliary functions. Finally, depletion of CCDC66 compromised Hedgehog and Wnt pathway activation and disrupted epithelial cell organization and polarity in two- and three-dimensional cultures. Collectively, we showed that CCDC66 regulates both ciliary and non-ciliary processes through diverse mechanisms involving microtubules, actin, and vesicular trafficking, providing insights into the pathologies associated with CCDC66.
CCDC66 regulates primary cilium length and signaling via interactions with transition zone and axonemal proteins
(Company of Biologists, 2023) Odabaşı, Ezgi; Çonkar, Deniz; Deretic, Jovana; Batman, Umut; Karalar, Elif Nur Fırat; Frikstad, Kari-Anne M.; Patzke, Sebastian; Department of Molecular Biology and Genetics; Yes; College of Sciences
The primary cilium is a microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome or cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based ciliary axoneme is assembled with a proper length and structure, particularly in terms of the activity of microtubule-associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome or cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium biogenesis. CCDC66 depletion in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the ciliopathy-linked MAPs CEP104 and CSPP1, and regulates axonemal length and Hedgehog pathway activation. Moreover, CCDC66 is required for the basal body recruitment of transition zone proteins and intraflagellar transport B (IFT-B) machinery. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium and provide insight into how ciliary MAPs and subcompartments cooperate to ensure assembly of functional cilia.
