Biology subjects

Jerkovic, I.

Publications and source records attributed to Jerkovic, I..

4 recordsLinked to original sources

bioRxiv2026

Algal-derived extracts act as selective ecological filters shaping soil microbiomes, bacterial traits, and tomato performance under biotic stress

Modern agriculture faces the dual challenge of increasing food production while reducing reliance on synthetic inputs that degrade soil ecosystems and compromise long-term sustainability. Algal biomasses have emerged as promising biostimulants, yet their capacity to selectively modulate soil microbiomes and plant growth-promoting bacterial (PGPB) functions remains poorly understood. Here, we evaluated 17 phylogenetically and biochemically diverse macro- and microalgal extracts to determine their effects on soil microbial communities, bacterial functional traits, and tomato (Solanum lycopersicum) performance. Algal supplementation selectively restructured microbial communities without disrupting overall diversity, promoting taxa associated with plant-beneficial functions, including Bacillus, Pseudomonas, and Actinobacteria. In soil microcosms, specific treatments increased culturable bacterial abundance by up to [~]200-fold relative to the initial soil. Functional assays revealed strong extract- and strain-dependent responses. Siderophore production and ACC-associated activity were the most consistently stimulated traits, whereas auxin production, biofilm formation, and proline synthesis showed more variable or context-dependent responses. Notably, Ulva sp. (AP11.2) enhanced siderophore production across the majority of isolates, with over four-fold increases in individual strains, while Arthrospira-derived extracts (NG4.1, N14.1) consistently promoted bacterial growth across multiple taxa. In contrast, extracts such as Nannochloropsis sp. (NG6.1) and Tetraselmis sp. (NG5.1) induced more selective or inhibitory responses, highlighting extract-dependent functional trade-offs. Integration of biochemical and biological datasets identified fatty acid composition as a key axis associated with microbial functional responses, whereas volatile organic compound profiles showed weaker and less consistent associations. These microbiome and functional shifts translated into improved plant performance, with algal treatments increasing tomato growth and reducing mortality by approximately 20% under non-sterile soil conditions characterized by pathogen-associated pressure. Together, these findings demonstrate that algal extracts act as selective modulators of soil microbiomes, enhancing specific bacterial functions and improving plant performance in a context-dependent manner. This work provides a mechanistic framework for the development of targeted algal-based biostimulants aimed at reducing agrochemical inputs and advancing microbiome-informed agriculture.

ecology↗

bioRxiv2024

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

1Upon differentiation chromatin rewires to reflect its new cellular identity and function. While it is widely known that this process involves cooperative changes in transcription, chromatin composition and 3D conformation, it is unclear what exactly drives these changes and how they influence one another. Here we used ESC-to-NPC differentiation to study rewiring at a 3 Mb large neuronal Zfp608 locus. During this process, this large chromatin domain splits in half right at the Zfp608 promoter, local chromatin gets littered with activating marks, compacts in 3D space and Zfp608 abounds in transcription. We investigated the cis and trans elements using capture Hi-C (cHi-C), extensive biophysical modelling, and 3-colour 3D-FISH with technical and analytical breakthroughs and found that transcription abundance modulates the contacts in the region as well as the insulation at the domain split. Furthermore, we found a genetic element we named scaffolding element, with a dual enhancer and architectural function that is essential for chromatin rewiring and loop formation at the NPC stage. The loss of this element disrupts the formation of all local NPC-loops irrespective if they are anchored in this element or not, highlighting the hierarchical relationship between elements that act as loop anchors. Furthermore, we uncovered that the scaffolding function, although driven by multiple mechanisms, can form loops independent of loop-extrusion and that other molecular attractions were necessary to form NPC-specific contacts in the region. Together, these results demonstrate that a hierarchy of genetic elements in cis allows successful rewiring during differentiation and that multiple trans acting elements contribute to make this rewiring efficient.

cell biology↗

bioRxiv2019

Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression

The genome is organized in megabase-sized three-dimensional units, called Topologically Associated Domains (TADs), that are separated by boundaries. TADs bring distant cis-regulatory elements into proximity, a process dependent on the cooperative action of cohesin and the DNA binding factor CTCF. Surprisingly, genome-wide depletion of CTCF has little effect on transcription, yet structural variations affecting TADs have been shown to cause gene misexpression and congenital disease. Here, we investigate TAD function in vivo in mice by systematically editing components of TAD organization at the Sox9/Kcnj locus. We find that TADs are formed by a redundant system of CTCF sites requiring the removal of all major sites within the TAD and at the boundary for two neighboring TADs to fuse. TAD fusion resulted in leakage of regulatory activity from the Sox9 to the Kcnj TAD, but no major changes in gene expression. This indicates that TAD structures provide robustness and precision, but are not essential for developmental gene regulation. Gene misexpression and resulting disease phenotypes, however, were attained by re-directing regulatory activity through inversions and/or the re-positioning of boundaries. Thus, efficient re-wiring of enhancer promoter interaction and aberrant disease causing gene activation is not induced by a mere loss of insulation but requires the re-direction of contacts.

genetics↗

bioRxiv2019

Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development

Long-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time. However, in some cases proximity coincides with gene activation, whereas in others preformed topologies already exist before activation. In this study, we investigate the preformed configuration underlying the regulation of the Shh gene by its unique limb enhancer, the ZRS, in vivo during mouse development. Abrogating the constitutive transcription covering the ZRS region led to a shift within the Shh-ZRS contacts and a moderate reduction in Shh transcription. Deletion of the CTCF binding sites around the ZRS resulted in a loss of the Shh-ZRS preformed interaction and a 50% decrease in Shh expression but no phenotype, suggesting an additional, CTCF-independent mechanism of promoter-enhancer communication. This residual activity, however, was diminished by combining the loss of CTCF binding with a hypomorphic ZRS allele resulting in severe Shh loss-of-function and digit agenesis. Our results indicate that the preformed chromatin structure of the Shh locus is sustained by multiple components and acts to reinforce enhancer-promoter communication for robust transcription.

developmental biology↗