Ivana Cavka

All Publications

• SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification SCIENCE ADVANCES Padovani, F., Cavka, I., Neves, A., Lopez, C., Al-Refaie, N., Bolcato, L., Chatzitheodoridou, D., Chadha, Y., Lagos, P., Stegmaier, T., Su, X. A., Lengefeld, J., Cabianca, D. S., Koehler, S., Schmoller, K. M. 2026; 12 (35): eadw3811

  Abstract

  The analysis of spot-like structures is a widespread task in microscopy image analysis. Existing solutions are typically specific to single applications and do not use multidimensional information, often leaving manual annotation as the only option. Here, we present SpotMAX, a generalist AI-assisted framework for automated spot detection and quantification. SpotMAX detects spots in three-dimensional (3D) data and leverages the full scope of multidimensional datasets with an easy-to-use graphical user interface and a framework for cell segmentation and tracking. Tested on a large 3D dataset, SpotMAX outperforms or is on par with state-of-the-art tools and expert human annotators. We applied SpotMAX across diverse experimental questions, ranging from meiotic crossover events in Caenorhabditis elegans to mitochondrial DNA dynamics in Saccharomyces cerevisiae and telomere length in mouse stem cells, leading to new biological insights. With its flexibility in integrating other AI models into a holistic analysis workflow, we anticipate that SpotMAX will become the standard for spot analysis in microscopy data.

  View details for DOI 10.1126/sciadv.adw3811

  View details for Web of Science ID 001862904100012

  View details for PubMedID 42664352

  View details for PubMedCentralID PMC13524050

• The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control. bioRxiv : the preprint server for biology Anderson, E. C., Rahmaninejad, H., Aljahani, A., Arnold, E. M., Adachi, A. S., Shah, R., Hansen, K. L., Cavka, I., Boettiger, A. N., Fudenberg, G., Nora, E. P. 2026

  Abstract

  Enhancers have been proposed to act as privileged loading sites for cohesin, raising the idea that they actively fold the genome to engage distal target promoters for transcription. Supporting this idea, NIPBL/MAU2, which is required for cohesin loading, binds at enhancers in mouse embryonic stem cells. However, we find that driving cohesin recruitment near an enhancer strongly inhibits transcription from its target distal promoter, indicating that strong focal cohesin loading at enhancers is not compatible with their long-range regulatory functions. Quantitative experiments and biophysical modeling further indicate that cohesin loading at enhancers does not make major contributions to genome-wide cohesin binding and chromosome folding patterns. Instead, cohesin must load throughout the genome to extrude it, regardless of enhancer proximity, with the major determinants of cohesin traffic being extrusion barriers such as transcription and clustered CTCF sites. These findings indicate that enhancer function is largely ancillary to the general mechanisms of chromosome folding, informing further study of the relationship between genome architecture and transcriptional regulation.

  View details for DOI 10.64898/2026.01.20.700462

  View details for PubMedID 41648525

  View details for PubMedCentralID PMC12871789

• Multi-step implementation of meiotic crossover patterning. bioRxiv : the preprint server for biology Čavka, I., Woglar, A., Wu, Y. L., Durmus, E. B., Sloat, L., Gros, A., Piñeiro López, C., Hecht, F., Villeneuve, A. M., Ries, J., Köhler, S. 2025

  Abstract

  Crossover formation during meiosis is a tightly controlled process in which genetic information is exchanged between homologous chromosomes to increase the diversity of the progeny. In this process, an excess of double-strand breaks is introduced, but only a limited subset is ultimately processed into crossovers. Imbalances in the distribution of crossovers can lead to errors in chromosome segregation, with devastating consequences on the health of the progeny. However, the selection of which breaks are designated to become crossovers is still poorly understood, as both its timing and the ultimate molecular mechanisms are under debate. Here, we used 3D dual-color single-molecule localization microscopy and real-time confocal imaging, combined with advanced image analysis, to investigate the timing and mechanism of crossover designation in C. elegans. We show that meiotic crossover patterning is not established by a single decision point but depends on a dynamic, multi-layered regulation process. An initial, early selection process restricts potential crossovers to a small subset of double-strand break sites that already exhibit basic patterning features, including assurance and interference. A second, later step fine-tunes this pattern to ultimately ensure genome integrity and promote accurate chromosome segregation. Real-time imaging reveals that although the full process takes more than seven hours, key molecular events occur within minutes, highlighting how rapid local dynamic changes can give rise to an overall slow but extremely robust crossover regulation program.

  View details for DOI 10.1101/2025.11.12.687980

  View details for PubMedID 41292815

  View details for PubMedCentralID PMC12642587

• Bloom helicase contributes to successful crossover formation with both catalytic and structural roles in Caenorhabditis elegans meiosis NUCLEIC ACIDS RESEARCH Geetha, S., Cavka, I., Dello Stritto, M., Graf, A., Macha, T., Krakolinig, H., Kohler, S., Jantsch, V. 2025; 53 (19)

  Abstract

  Crossover (CO)-biased repair of meiotic DNA double-strand breaks is essential for proper chromosome segregation. However, only a subset of programmed induced DSBs is repaired as COs, while the rest is processed into non-COs. The Bloom-Topoisomerase 3-RMI1/2 complex is well documented to disassemble joint recombination intermediates into non-COs, but its pro-CO activities are less well understood. Here, we investigate how the pro-CO activities of the Caenorhabditis elegans Bloom helicase ortholog HIM-6 contribute to meiotic recombination by studying a catalytically inactive mutant. We show that HIM-6 helicase activity is required to provide a continuous flux of substrates for CO formation, probably via its unwinding activities, and that a structural role is sufficient to channel intermediates into the preferred pathway to generate correctly positioned COs. We provide evidence that the catalytic activity of Bloom helicase influences the geometry of the joint DNA molecules (double Holliday junctions (dHJ)). Localization of the signal for the dHJ-stabilizing complex MutSγ was more restricted, and epistasis experiments suggest that an altered geometry impedes the efficient processing of joint DNA molecules to generate CO-biased cleavage products.

  View details for DOI 10.1093/nar/gkaf1030

  View details for Web of Science ID 001597469800001

  View details for PubMedID 41123207

  View details for PubMedCentralID PMC12541369

• Crossovers are regulated by a conserved and disordered synaptonemal complex domain NUCLEIC ACIDS RESEARCH Neves, A., Cavka, I., Rausch, T., Koehler, S. 2025; 53 (4)

  Abstract

  During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chromosome missegregation and genomic instability in the progeny. Here we show that this regulation of COs depends on a disordered and conserved domain within the synaptonemal complex (SC). This domain is located at the C-terminus of the central element protein SYP-4 in Caenorhabditis elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both CO assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of CO events. Instead, we discovered that nine conserved phenylalanines are required to recruit a pro-CO factor predicted to be an E3 ligase and regulate the physical properties of the SC. We propose that this conserved and disordered domain plays a crucial role in maintaining the SC in a state that allows transmitting signals to regulate CO formation. While the underlying mechanisms remain to be fully understood, our findings align with existing models suggesting that the SC plays a critical role in determining the number and distribution of COs along chromosomes, thereby safeguarding the genome for future generations.

  View details for DOI 10.1093/nar/gkaf095

  View details for Web of Science ID 001424370500004

  View details for PubMedID 39964475

  View details for PubMedCentralID PMC11833701

• Skp1 proteins are structural components of the synaptonemal complex in <i>C. elegans</i> SCIENCE ADVANCES Blundon, J. M., Cesar, B. I., Bae, J., Cavka, I., Haversat, J., Ries, J., Koehler, S., Kim, Y. 2024; 10 (7): eadl4876

  Abstract

  The synaptonemal complex (SC) is a zipper-like protein assembly that links homologous chromosomes to regulate recombination and segregation during meiosis. The SC has been notoriously refractory to in vitro reconstitution, thus leaving its molecular organization largely unknown. Here, we report a moonlighting function of two paralogous S-phase kinase-associated protein 1 (Skp1)-related proteins (SKR-1 and SKR-2), well-known adaptors of the Skp1-Cul1-F-box (SCF) ubiquitin ligase, as the key missing components of the SC in Caenorhabditis elegans. SKR proteins repurpose their SCF-forming interfaces to dimerize and interact with meiosis-specific SC proteins, thereby driving synapsis independent of SCF activity. SKR-1 enables the formation of the long-sought-after soluble complex with previously identified SC proteins in vitro, which we propose it to represent a complete SC building block. Our findings demonstrate how a conserved cell cycle regulator has been co-opted to interact with rapidly evolving meiotic proteins to construct the SC and provide a foundation for understanding its structure and assembly mechanisms.

  View details for DOI 10.1126/sciadv.adl4876

  View details for Web of Science ID 001189022400020

  View details for PubMedID 38354250

  View details for PubMedCentralID PMC10866564

• Super-Resolution Microscopy of the Synaptonemal Complex within the <i>Caenorhabditis</i> <i>elegans</i> Germline JOVE-JOURNAL OF VISUALIZED EXPERIMENTS Cavka, I., Power, R. M., Walsh, D., Zimmermann, T., Koehler, S. 2022

  Abstract

  During meiosis, homologous chromosomes must recognize and adhere to one another to allow for their correct segregation. One of the key events that secures the interaction of homologous chromosomes is the assembly of the synaptonemal complex (SC) in meiotic prophase I. Even though there is little sequence homology between protein components within the SC among different species, the general structure of the SC has been highly conserved during evolution. In electron micrographs, the SC appears as a tripartite, ladder-like structure composed of lateral elements or axes, transverse filaments, and a central element. However, precisely identifying the localization of individual components within the complex by electron microscopy to determine the molecular structure of the SC remains challenging. By contrast, fluorescence microscopy allows for the identification of individual protein components within the complex. However, since the SC is only ~100 nm wide, its substructure cannot be resolved by diffraction-limited conventional fluorescence microscopy. Thus, determining the molecular architecture of the SC requires super-resolution light microscopy techniques such as structured illumination microscopy (SIM), stimulated-emission depletion (STED) microscopy, or single-molecule localization microscopy (SMLM). To maintain the structure and interactions of individual components within the SC, it is important to observe the complex in an environment that is close to its native environment in the germ cells. Therefore, we demonstrate an immunohistochemistry and imaging protocol that enables the study of the substructure of the SC in intact, extruded Caenorhabditis elegans germline tissue with SMLM and STED microscopy. Directly fixing the tissue to the coverslip reduces the movement of the samples during imaging and minimizes aberrations in the sample to achieve the high resolution necessary to visualize the substructure of the SC in its biological context.

  View details for DOI 10.3791/64363

  View details for Web of Science ID 000909465300037

  View details for PubMedID 36190293

  View details for PubMedCentralID PMC7614930

• Global fitting for high-accuracy multi-channel single-molecule localization NATURE COMMUNICATIONS Li, Y., Shi, W., Liu, S., Cavka, I., Wu, Y., Matti, U., Wu, D., Koehler, S., Ries, J. 2022; 13 (1): 3133

  Abstract

  Multi-channel detection in single-molecule localization microscopy greatly increases information content for various biological applications. Here, we present globLoc, a graphics processing unit based global fitting algorithm with flexible PSF modeling and parameter sharing, to extract maximum information from multi-channel single molecule data. As signals in multi-channel data are highly correlated, globLoc links parameters such as 3D coordinates or photon counts across channels, improving localization precision and robustness. We show, both in simulations and experiments, that global fitting can substantially improve the 3D localization precision for biplane and 4Pi single-molecule localization microscopy and color assignment for ratiometric multicolor imaging.

  View details for DOI 10.1038/s41467-022-30719-4

  View details for Web of Science ID 000808000200008

  View details for PubMedID 35668089

  View details for PubMedCentralID PMC9170706

• Identification of novel synaptonemal complex components in <i>C. elegans</i> JOURNAL OF CELL BIOLOGY Hurlock, M. E., Cavka, I., Kursel, L. E., Haversat, J., Wooten, M., Nizami, Z., Turniansky, R., Hoess, P., Ries, J., Gall, J. G., Rog, O., Koehler, S., Kim, Y. 2020; 219 (5)

  Abstract

  The synaptonemal complex (SC) is a tripartite protein scaffold that forms between homologous chromosomes during meiosis. Although the SC is essential for stable homologue pairing and crossover recombination in diverse eukaryotes, it is unknown how individual components assemble into the highly conserved SC structure. Here we report the biochemical identification of two new SC components, SYP-5 and SYP-6, in Caenorhabditis elegans. SYP-5 and SYP-6 are paralogous to each other and play redundant roles in synapsis, providing an explanation for why these genes have evaded previous genetic screens. Superresolution microscopy reveals that they localize between the chromosome axes and span the width of the SC in a head-to-head manner, similar to the orientation of other known transverse filament proteins. Using genetic redundancy and structure-function analyses to truncate C-terminal tails of SYP-5/6, we provide evidence supporting the role of SC in both limiting and promoting crossover formation.

  View details for DOI 10.1083/jcb.201910043

  View details for Web of Science ID 000531028900014

  View details for PubMedID 32211899

  View details for PubMedCentralID PMC7199856