Imaging Nuclear Clusters in Live Zebrafish Embryos

Shivali Dongre ¹, Lennart Hilbert ^2 3, Nadine L Vastenhouw ⁴

. 2025:2923:89-117.

• PMID: 40418446
• DOI: 10.1007/978-1-0716-4522-2_7

Abstract

The transcriptional machinery of a cell is often not homogenously distributed but rather forms clusters in the nucleus. These clusters are important for gene expression, but how they form and function is often not clear. The zebrafish embryo provides an excellent system to study these clusters of transcriptional machinery, because embryos are transparent and develop rapidly, making it easy to track proteins as they cluster and perform their function. Here, we provide a protocol for how to image nuclear clusters in living zebrafish embryos. The protocol includes information on the selection and encoding of proteins and fluorophores, embryo-embedding for live-cell microscopy, the use of a spinning disk microscope, staging of embryos post image acquisition, and image analysis. While the protocol is written in the context of our work with early zebrafish embryos, many of the tools will be useful in other contexts.

What is the current bottleneck in mapping molecular interaction networks?

Michael A Skinnider, Katja Luck, M Shahid Mukhtar, Martin Garrido-Rodriguez, Julio Saez-Rodriguez, Jolanda van Leeuwen, Pedro Beltrao, Anne-Ruxandra Carvunis, Mikko Taipale, Andrew Emili, Martha L Bulyk, Nevan J Krogan

• PMID: 40403700
• DOI: 10.1016/j.cels.2025.101295

No abstract available

PubMed Disclaimer

Conflict of interest statement

Declaration of interests A.-R.C. is a member of the scientific advisory board for ProFound Therapeutics. J.S.-R. reports in the last 3 years funding from GSK and Pfizer and fees/honoraria from Travere Therapeutics, STADApharm, Astex, Pfizer, Owkin, Moderna, and Grunenthal. M.A.S. is a member of the Rutgers Cancer Institute of New Jersey (RCINJ). The Krogan laboratory has received research support from Vir Biotechnology, F. Hoffmann-La Roche, and Rezo Therapeutics. N.J.K. has a financially compensated consulting agreement with Maze Therapeutics. He is the president and is on the board of directors of Rezo Therapeutics, and he is a shareholder in Tenaya Therapeutics, Maze Therapeutics, Rezo Therapeutics, and GEn1E Lifesciences.

An integrated anatomical, functional and evolutionary view of the Drosophila olfactory system

Richard Benton ^# 1, Jérôme Mermet ^# 2, Andre Jang ³, Keita Endo ⁴, Steeve Cruchet ², Karen Menuz ^5 6

. 2025 May 19.

 doi: 10.1038/s44319-025-00476-8. Online ahead of print.

• PMID: 40389758
• DOI: 10.1038/s44319-025-00476-8

Free article

Abstract

The Drosophila melanogaster olfactory system is one of the most intensively studied parts of the nervous system in any animal. Composed of ~50 independent olfactory neuron classes, with several associated hygrosensory and thermosensory pathways, it has been subject to diverse types of experimental analyses. However, synthesizing the available information is limited by the incomplete data and inconsistent nomenclature found in the literature. In this work, we first “complete” the peripheral sensory map through the identification of a previously uncharacterized antennal sensory neuron population expressing Or46aB, and the definition of an exceptional “hybrid” olfactory neuron class comprising functional Or and Ir receptors. Second, we survey developmental, anatomical, connectomic, functional, and evolutionary studies to generate an integrated dataset and associated visualizations of these sensory neuron pathways, creating an unprecedented resource. Third, we illustrate the utility of the dataset to reveal relationships between different organizational properties of this sensory system, and the new questions these stimulate. Such examples emphasize the power of this resource to promote further understanding of the construction, function, and evolution of these neural circuits.

Further delineation of the SCAF4-associated neurodevelopmental disorder

Cosima M Schmid ^1 2, Anne Gregor ^1 2, Anna Ruiz ³, Carmen Manso Bazús ³, Isabella Herman ^4 5 6, Farah Ammouri ⁷, Urania Kotzaeridou ⁸, Vanda McNiven ⁹, Lucie Dupuis ¹⁰, Katharina Steindl ¹¹, Anaïs Begemann ¹¹, Anita Rauch ¹¹, Aude-Annick Suter ¹¹, Bertrand Isidor ¹², Sandra Mercier ¹², Mathilde Nizon ¹², Benjamin Cogné ¹², Wallid Deb ¹², Thomas Besnard ¹², Tobias B Haack ^13 14, Ruth J Falb ¹³, Amelie J Müller ¹³, Tobias Linden ¹⁵, Chad R Haldeman-Englert ¹⁶, Charlotte W Ockeloen ¹⁷, Francesca Mattioli ¹⁸, Alexandre Reymond ¹⁸, Nazia Ibrahim ¹⁹, Shagufta Naz ¹⁹, Elodie Lacaze ²⁰, Jennifer A Bassetti ²¹, Julia Hoefele ²², Theresa Brunet ²², Korbinian M Riedhammer ^22 23, Houda Z Elloumi ²⁴, Richard Person ²⁴, Fanggeng Zou ²⁴, Juliette J Kahle ²⁴, Kirsten Cremer ²⁵, Axel Schmidt ²⁵, Marie-Ange Delrue ²⁶, Pedro M Almeida ²⁷, Fabiana Ramos ^27 28, Siddharth Srivastava ²⁹, Aisling Quinlan ²⁹, Stephen Robertson ³⁰, Eva Manka ³¹, Alma Kuechler ³², Stephanie Spranger ³³, Malgorzata J M Nowaczyk ³⁴, Reem M Elshafie ³⁵, Hind Alsharhan ^35 36, Paul R Hillman ³⁷, Leslie A Dunnington ³⁷, Hilde M H Braakman ³⁸, Shane McKee ³⁹, Angelica Moresco ⁴⁰, Andrea-Diana Ignat ⁴⁰, Ruth Newbury-Ecob ⁴¹, Guillaume Banneau ⁴², Olivier Patat ⁴², Jeffrey Kuerbitz ^6 43, Susan Rzucidlo ⁴⁴, Susan S Sell ⁴⁴, Patricia Gordon ⁴⁴, Sarah Schuhmann ⁴⁵, André Reis ^45 46, Yosra Halleb ⁴⁷, Radka Stoeva ⁴⁷, Boris Keren ⁴⁸, Zainab Al Masseri ⁴⁹, Zeynep Tümer ^50 51, Sophia Hammer-Hansen ⁵², Sofus Krüger Sølyst ⁵², Connolly G Steigerwald ⁵³, Nicolas J Abreu ⁵³, Helene Faust ⁵⁴, Amica Müller-Nedebock ⁵⁴, Frédéric Tran Mau-Them ^55 56, Heinrich Sticht ⁵⁷, Christiane Zweier ^58 59

. 2025 May;33(5):588-594.

• PMID: 39668183
• PMCID: PMC12048650
• DOI: 10.1038/s41431-024-01760-2

Abstract

While mostly de novo truncating variants in SCAF4 were recently identified in 18 individuals with variable neurodevelopmental phenotypes, knowledge on the molecular and clinical spectrum is still limited. We assembled data on 50 novel individuals with SCAF4 variants ascertained via GeneMatcher and personal communication. With detailed evaluation of clinical data, in silico predictions and structural modeling, we further characterized the molecular and clinical spectrum of the autosomal dominant SCAF4-associated neurodevelopmental disorder. The molecular spectrum comprises 25 truncating, eight splice-site and five missense variants. While all other truncating variants were classified as pathogenic/likely pathogenic, significance of one C-terminal truncating variant, one splice-site variant and the missense variants remained unclear. Three missense variants in the CTD-interacting domain of SCAF4 were predicted to destabilize the domain. Twenty-three variants occurred de novo, and variants were inherited in 13 cases. Frequent clinical findings were mild developmental delay with speech impairment, seizures, and skeletal abnormalities such as clubfoot, scoliosis or hip dysplasia. Cognitive abilities ranged from normal IQ to severe intellectual disability (ID), with borderline to mild ID in the majority of individuals. Our study confirms the role of SCAF4 variants in neurodevelopmental disorders and further delineates the associated clinical phenotype.

Estrogen Receptors/E2F1/CDKN3 Axis Protects from UV-induced Skin Cancers in Females

Céline Lukowicz, Carine Winkler, Catherine Roger, Joanna C Fowler, Yi-Chien Tsai, Joachim Meuli, Stéphanie Claudinot, Yun-Tsan Chang, Christoph Iselin,  View ORCID ProfilePhilip H Jones, Emmanuella Guenova, Paris Jafari, Liliane Michalik

doi: https://doi.org/10.1101/2025.02.12.637819

This article is a preprint and has not been certified by peer review [what does this mean?].

Abstract

Men have a significantly higher risk of developing cutaneous squamous cell carcinoma (SCC) compared to women, but models and comprehensive analysis of signaling pathways highlighting this sexual dimorphism are missing. In this study, we display a UV-induced SCC model in hairless mice recapitulating this sex difference, with enhanced SCC development in males. While UV-induced DNA damage is similar between sexes, we uncovered sex-specific responses in epidermal cell proliferation and differentiation. Using global transcriptional profile analyses, we identified E2F transcription factors as key sex-specific markers involved in the proliferative response to UV. Notably, E2F1/2, along with their target gene CDKN3, were selectively downregulated in female mice and human epidermis following UV exposure. Mechanistically, UV-induced and sex-specific modulation of E2F1 and CDKN3 expression is mediated by Estrogen Receptors. Lastly, low levels of CDKN3 in head and neck SCC are observed exclusively in female patients correlating with better prognosis. These findings shed new light on fundamental mechanisms protecting women from cancer after carcinogen exposure and could lead to better sex-targeted preventive and therapeutic strategies in SCC and other malignancies.

[Preprint]. 2025 Mar 25:2025.03.23.644808.doi: 10.1101/2025.03.23.644808.

Canalization of flower production across thermal environments requires Florigen and CLAVATA signaling

Elizabeth S Smith ¹, Amala John ¹, Andrew C Willoughby ¹, Daniel S Jones ¹, Vinicius C Galvão ², Christian Fankhauser ², Zachary L Nimchuk ^1 3

Affiliations Expand

• PMID: 40196672
• PMCID: PMC11974719
• DOI: 10.1101/2025.03.23.644808

Abstract

The ability to maintain invariant developmental phenotypes across disparate environments is termed canalization, but few examples of canalization mechanisms are described. In plants, robust flower production across environmental gradients contributes to reproductive success and agricultural yields. Flowers are produced by the shoot apical meristem (SAM) in an auxin-dependent manner following the switch from vegetative growth to the reproductive phase. While the timing of this phase change, called the floral transition, is sensitized to numerous environmental and endogenous signals, flower formation itself is remarkably invariant across environmental conditions. Previously we found that CLAVATA peptide signaling promotes auxin-dependent flower primordia formation in cool environments, but that high temperatures can restore primordia formation through unknown mechanisms. Here, we show that heat promotes floral primordia patterning and formation in SAMs not by increased auxin production, but through the production of the mobile flowering signal, florigen, in leaves. Florigen, which includes FLOWERING LOCUS T (FT) and its paralog TWIN SISTER OF FT (TSF) in Arabidopsis thaliana, is necessary and sufficient to buffer flower production against the loss of CLAVATA signaling and promotes heat-mediated primordia formation through specific SAM expressed transcriptional regulators. We find that sustained florigen production is necessary for continuous flower primordia production at warmer temperatures, contrasting florigen’s switch-like control of floral transition. Lastly, we show that CLAVATA signaling and florigen synergize to canalize flower production across broad temperature ranges. This work sheds light on the mechanisms governing the canalization of plant development and provides potential targets for engineering crop plants with improved thermal tolerances.