Research Project: Spatiotemporal regulation of centriolar satellite homeostasis
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Contributors
Funders
ID
EC.00177
Authors
Karalar, Elif Nur Fırat
Faculty Member
Publications
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.
Kinase activity of DYRK family members is required for regulating primary cilium length, stability and morphology
(Nature Research, 2025) Arslanhan, Melis Dilara; Karalar, Elif Nur Fırat; Topçu, Ebru; Arslanhan, Melis Dilara; Department of Molecular Biology and Genetics; School of Medicine; Yes; Topçu, Ebru; SCHOOL OF MEDICINE; College of Sciences
The dual-specificity tyrosine-phoshorylation-regulated kinase (DYRK) family are multifunctional enzymes crucial for diverse cellular processes, including signaling through the primary cilium. Their dysregulation has been implicated in various cancers and developmental disorders, highlighting the need to define their interactors and cellular functions to inform targeted therapeutics. In this study, we generate the proximity interactome of DYRK3, identifying 178 proteins involved in a range of cellular processes, including primary cilium biogenesis. We then investigate the specific role of DYRK3 and its cooperation with other DYRK family members in cilium assembly and maintenance. RNAi-mediated depletion of DYRK3 and pharmacological inhibition of DYRK kinase activity using GSK-626616 (GSK) lead to elongation of the cilium, particularly its distal segment. GSK treatment also induces ciliary defects, length fluctuations, and increased ectocytosis. Co-depletion and phenotypic rescue experiments reveal that DYRK2 and DYRK3 cooperate in regulating cilium length. Moreover, inhibiting or depleting known cilium length regulators, or quantifying their ciliary levels in GSK-treated cells, reveal functional relationships of DYRKs to centriolar satellites and the IFT complex. Collectively, our findings uncover regulatory roles for DYRK3 and DYRK kinase activity in the assembly and maintenance of primary cilium with proper length, stability, and morphology.
Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes
(WILEY, 2024) Begar, Efe; Karalar, Elif Nur Fırat; Seyrek, Ece; 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 ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.
Centriolar satellites are dynamic membrane-less organelles that assemble via a hierarchical pathway
(Cold Spring Harbor Laboratory, 2025) Seyrek, Ece; Nacaklı, Selin; Arslanhan, Melis Dilara; Odabaşı, Ezgi; Karalar, Elif Nur Fırat; Begar, Efe; Begar, Efe; Nacaklı, Selin; Seyrek, Ece; Arslanhan, Melis Dilara; Department of Molecular Biology and Genetics; School of Medicine; Yes; College of Sciences; SCHOOL OF MEDICINE
Centriolar satellites (CS) are ubiquitous, membrane-less organelles recognized for their dynamic organelle crosstalk, plasticity, diverse functions and links to developmental and neuronal diseases. Despite their significance, the mechanisms underlying CS assembly and homeostasis are unknown. Here, we developed in vitro and cellular CS biogenesis assays to spatiotemporally quantify the homeostatic properties of CS granules during assembly and maintenance. These assays revealed that CS assemble via a hierarchical pathway initiated by PCM1 scaffold formation followed by sequential recruitment of CS proteins. We discovered that PCM1 inherently forms granules through multimerization and phase separation, processes regulated by cytoskeleton and ciliopathy proteins. Additionally, PCM1 scaffold and clients are organized into subdomains within CS granules with distinct composition and dynamics. Selectively disrupting CS granule properties impaired the ciliary signaling functions of CS. Collectively, our results provide comprehensive insight into CS biogenesis and establish a conceptual framework and new tools to investigate context-dependent CS functions and their deregulation in disease. The mechanisms identified for CS may also explain the specificity and plasticity of other membrane-less organelles.
