Biology subjects

Cavka, I.

Publications and source records attributed to Cavka, I..

5 recordsLinked to original sources

bioRxiv2026

The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control

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.

molecular biology↗

bioRxiv2025

Multi-step implementation of meiotic crossover patterning

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, high-lighting how rapid local dynamic changes can give rise to an overall slow but extremely robust crossover regulation program.

cell biology↗

bioRxiv2024

SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification

The analysis of spot-like structures is a widespread task in microscopy-based cell biology. Existing solutions are typically specific to single applications and do not use multi-dimensional information from 5D datasets. Therefore, experimental scientists often resort to subjective manual annotation. Here, we present SpotMAX, a generalist AI-driven framework for automated spot detection and quantification. SpotMAX leverages the full scope of multi-dimensional datasets with an easy-to-use interface and an embedded framework for cell segmentation and tracking. SpotMAX outperforms state-of-the-art tools, and in some cases, even expert human annotators. We applied SpotMAX across diverse experimental questions, ranging from meiotic crossover events in C. elegans to mitochondrial DNA dynamics in S. cerevisiae and telomere length in mouse stem cells, leading to new biological insights. With its flexibility in integrating AI workflows, we anticipate that SpotMAX will become the standard for spot analysis in microscopy data. Source code: https://github.com/SchmollerLab/SpotMAX

cell biology↗

bioRxiv2024

Crossovers are regulated by a conserved and disordered synaptonemal complex domain

To ensure the accurate segregation of homologous chromosomes and enhance the genetic diversity in the progeny, meiosis depends on the formation of crossovers between homologous chromosomes. The number and distribution of these crossovers must be precisely regulated through crossover assurance and interference to prevent chromosome missegregation and genomic instability. Here we show that the regulation of crossovers depends on a disordered domain within the synaptonemal complex, which is highly conserved. This domain is located at the C-terminus of the central element protein SYP-4 in C. elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both crossover assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of crossover events. Instead, we discovered that nine conserved phenylalanines recruit a pro-crossover factor predicted to be an E3 ligase and regulate the physical properties of the synaptonemal complex. We propose that this conserved and disordered domain plays a crucial role in maintaining the synaptonemal complex in an activated state to promote crossing-over. This activation allows the synaptonemal complex to regulate the number and distribution of crossovers along chromosomes, thereby protecting the genome for future generations.

cell biology↗

bioRxiv2023

Skp1 proteins are structural components of the synaptonemal complex in C. elegans

The synaptonemal complex (SC) is a hallmark of meiotic prophase that plays a crucial role in regulating crossovers between homologous chromosomes. Here, we demonstrate that two Skp1-related proteins in C. elegans, SKR-1 and SKR-2, serve as structural components of the SC, independent of their canonical functions within the Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. SKR-1 and SKR-2 localize to the central region of the SC, and synapsis requires their dimerization through a hydrophobic interface that overlaps with the binding sites for CUL-1 and F-box proteins. Using in vitro reconstitution and in vivo analysis of mutant proteins, we show that SKR proteins interact with the other SC proteins using their C-terminal helices to form a soluble complex, which likely represents a basic building block for SC assembly. Our findings demonstrate how conserved Skp1 proteins are repurposed as part of the SC and may provide insight into how synapsis is coupled to cell cycle progression.

cell biology↗