Elif Nur Firat-Karalar

The next #DGZ Focus Workshop on #Cilia & #Centrosomes will take place November 25 (end of October is our DGZ meeting in HD). Join us for a great speaker line-up, and big thanks to David Mick @mick-lab.bsky.social & Dagmar Wachten @wachtenlab.bsky.social for organizing!

Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos Although specific transcription factors (TFs) are known to regulate cell fate decisions, the degree to which they can stimulate formation of specific cell organelles is less clear. We used a multiomic...

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Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos | Science www.science.org/doi/10.1126/...

If you're finishing PhD soon and thinking of postdocs, see below!

Especially if you're keen on combining biochemistry, imaging and cell biology, we are onto some exciting findings on molecules and mechanisms underlying a cytoplasmic division cycle autonomously of CDKs!!

Congratulations Moe!

Thank you, Irma, I completely agree. Beyond identifying the ciliary kinases, being able to define their specific substrates and phosphorylation sites would be an important next step. This has been especially challenging for DYRKs and large proteins like PCM1.

Many thanks to TUBITAK, @embo.org and @erc.europa.eu for funding and to Ebru Topcu for generating the DYRK3 interactome and Melis Arslanhan for its analysis and driving this story forward. We had great editorial experience at @commsbio.nature.com!

Through proximity mapping, loss-of-function and phenotypic rescue experiments, we found that DYRK kinases including DYRK3 ensure that the primary cilium assembles with proper length, stability and morphology.

A key turning point: we realized that GSK-626616, developed as a DYRK3 inhibitor, actually targets broader DYRK kinase activity. This led us to explore the roles of DYRKs, not just DYRK3, at the primary cilium.

Kinase activity of DYRK family members is required for regulating primary cilium length, stability and morphology - Communications Biology DYRK3 kinase interacts with multiple centriolar satellites and ciliary components to regulate axoneme length dynamics in cooperation with DYRK2.

New paper on DYRK kinases and primary cilium!
This project began with our interest in DYRK3’s relationship to centriolar satellites. But what started as a CS-focused story soon evolved into studying DYRK kinase activity during ciliogenesis.
nature.com/articles/s42...

Model for cellular functions and mechanisms of CCDC66. CCDC66 is a microtubule-stabilizing protein that maintains cilium integrity and size and facilitates vesicular transport at the ciliary base. Depletion of CCDC66 results in variations in cilia size due to compromised axonemal integrity, intraflagellar transport, and increased ectocytosis events involving the release of vesicles and fragments. CCDC66 may also support ciliary ectocytosis and length stability by regulating the actin cytoskeleton. Furthermore, disruptions in both microtubule stability and the actin cytoskeleton impair RAB11 and RAB5-mediated endocytosis and membrane recycling, affecting cell adhesion and the targeting of ciliary receptors. This disruption subsequently activates protein degradation pathways through RAB7-regulated late endocytosis, potentially involving RAB7 translocation to cilia to support ectocytosis. Collectively, these defects in protein transport, cilia function, and cell contacts contribute to compromised epithelial tissue integrity and multilumen formation in kidney tubules.

The #PrimaryCilium dynamically assembles & disassembles, but how is this controlled? @cytolabkoc.bsky.social shows that #ciliopathy linked protein Ccdc66 regulates both #cilium stability & length in epithelial cells via microtubules, actin & vesicular trafficking @plosbiology.org 🧪 plos.io/4mdTS4A

This study represents many years of dedicated effort and fantastic collaboration from my amazing team members Efe, Selin, Ece, Ezgi, and Melis!

4- Disrupting satellite homeostasis impairs their roles in signaling.
Our work introduces new concepts and tools to investigate satellite biology. Huge thanks to @erc.europa.eu
SatelliteHomeostasis funding that allowed us to tackle this fundamental question comprehensively!

1- Satellites assemble via a hierarchical pathway initiated by PCM1 scaffold formation followed by sequential recruitment of other satellite proteins.
2- PCM1 scaffold forms through multimerization and phase separation.
3- Satellite granules have distinct internal subdomains.

After unraveling the functional importance of centriolar satellites for centrosomes and cilia, we shifted focus to understand their own intrinsic biology as standalone organelles, which led to exciting new findings.

Exciting new preprint alert! Our latest research is a tour de force exploring the biology of centriolar satellites, membrane-less organelles essential for development and physiology. Below is a summary of our findings; dive into the full paper through this link 👇
biorxiv.org/content/10.1...

CCDC66 regulation of cytoskeleton and cilia stability is important for signaling and epithelial organization The primary cilium dynamically assembles and disassembles while maintaining structural stability and tightly regulated length, but the mechanisms that control this remain unclear. This study shows tha...

Our paper uncovering the role of the microtubule-associated protein CCDC66 in primary cilium stability and disassembly is now published in @plosbiology.org ! We discovered exciting new links between CCDC66, microtubules, actin, vesicular trafficking, and Wnt.

🔗 journals.plos.org/plosbiology/...

I’ll be visiting @wachtenlab.bsky.social’ lab at the Institute of Innate Immunity in Bonn this August for a mini‑sabbatical! I would love to connect with scientists in Bonn and beyond; please reach out if you’d like to chat, collaborate, or host a seminar.

Head of the Cell Biology and Biophysics Unit The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organisation, and one of the world’s leading research institutions. An intergovernmental organisation of 29 Member S...

EMBL Cell Biology and Biophysics department is searching for a new director. A major position to lead this field in Europe and beyond.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

ERC eligibility rules have changed! I'm among the last researchers awarded the ERC Starting Grant twice. The new rules could broaden applications but also increase competition, let's see how funding rates evolve!

As the incoming Chair of Biochemistry and Biophysics at Weill Cornell Medicine, I am looking for a Director of Research. Exciting opportunity for a PhD scientist to shape the future of this new Department! Apply here: jobs.weill.cornell.edu/NY/job/New-Y...

Even in the 'good' days, students/PDs on visas were always worried that they would run afoul of the law and be asked to leave. I know - I was on a student visa myself. I can't even begin to imagine their fear and anxiety now. Time for all university leaders to collectively step up and speak out!!

The MIT McGovern Institute’s story celebrating the 10th birthday of expansion microscopy (ExM). One highlight: ExM is not only easy to do, it’s easy to modify - so lots of people are altering and applying ExM for custom purposes, leading to unexpected innovations: mcgovern.mit.edu/2025/03/03/t...

iAPEX: Improved APEX-based proximity labeling for subcellular proteomics using an enzymatic reaction cascade Ascorbate peroxidase (APEX) is a versatile labeling enzyme used for live-cell proteomics at high spatial and temporal resolution. However, toxicity of its substrate hydrogen peroxide and background la...

Proud to share our work spear-headed by PhD student Tommy Sroka with major contributions by #xenopus expert Kerstin Feistel.

Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.

We had a wonderful New Year’s dinner! 2024 was full of great moments: I became an EMBO member, Leyla was born, we published important papers, presented at conferences, organized #advimaging2024, got a new microscope, welcomed new team members. Here is to more in 2025!

Sorry to miss #cellbio2024 as my 5-month-old isn't quite ready for transatlantic flights, But Cytolab is still represented! Don't miss Efe’s microsymposium talk & poster on centriolar satellites and Basak’s poster on non-ciliary functions of ciliopathy proteins.

Cilia structure and intraflagellar transport differentially regulate sensory response dynamics within and between C. elegans chemosensory neurons The relative contributions of intraflagellar transport (IFT) and cilia structure to sensory neuron responses remains unclear. This study reveals unexpected complexity in the contribution of IFT and ci...

🧪 Lab's latest!! Work by PD (and now PI) Alison Philbrook.
C. elegans sensory neurons have gorgeous #cilia. We’ve always thought that a) no cilia = no sensory responses, & b) no IFT = no cilia. Punchline is we thought wrong. Read paper for more!
#neuroscience
journals.plos.org/plosbiology/...

I'm excited to see that a photo of Leyla with me receiving my EMBO member certificate along with other members and EMBO Director Fiona Watt was shown in the photo gallery for the EMBO 60th anniversary celebration. What a wonderful memory for her!

Thank you Ula and the rest if the organizers for putting together such a fantastic meeting.

Could you please add me?

I look forward to visiting the University of Liverpool this Thursday to present our findings on centriolar satellites. I will also give the keynote talk and share our latest cilia findings at the UK Cilia Meeting on Friday.