Biology subjects

Dziasek, K.

Publications and source records attributed to Dziasek, K..

3 recordsLinked to original sources

bioRxiv2026

SirenScan reveals the conserved presence of siren RNAs and their evolutionary diversification across angiosperms

O_LISiren RNAs are exceptionally abundant reproductive small interfering RNAs (siRNAs), yet whether they represent a conserved feature of angiosperm reproduction has remained unclear because siren loci lack a standardized definition and identification strategy. C_LIO_LIWe developed SirenScan, a computational framework that integrates cumulation-based and density-based analyses to identify siren loci from small RNA sequencing data. Using SirenScan, we systematically compared ovule and vegetative tissues across representative angiosperm lineages, including the early-diverging angiosperm Nymphaea colorata. C_LIO_LIWe demonstrate that the presence of siren RNAs is a conserved feature of angiosperm ovules, although the degree of expression dominance varies substantially among species. Siren loci are consistently enriched within transposable elements (TEs), while the associated TE superfamilies and cis-regulatory motifs exhibit lineage-specific diversification. In Brassicaceae, siren loci share conserved CLASSY3-associated sequence motifs, whereas other angiosperm lineages display distinct motif compositions, suggesting evolutionary diversification of Polymerase IV targeting mechanisms. C_LIO_LIOur findings establish siren RNAs as a conserved component of the angiosperm reproductive small RNA landscape and support a model in which conserved RNA-directed DNA methylation machinery is coupled with lineage-specific regulatory mechanisms and transposon landscapes to shape siren locus evolution. SirenScan provides a robust and standardized framework for comparative studies of siren RNA biology and reproductive epigenomics across plant species. C_LI

plant biology↗

bioRxiv2021

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We have identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing hybridization barriers in crosses between different Capsella species, thus potentially emerging as a novel strategy for producing triploids and interspecific hybrids with high agronomical interest. One sentence summaryGenome-wide loss of DNA methylation induced by 5-Azacytidine allows bypassing interploidy and interspecific hybridization barriers in Arabidopsis and Capsella.

plant biology↗

bioRxiv2020

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm

Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTLs for the underlying cause of hybrid incompatibility in Capsella revealed three QTLs that were close to pericentromeric regions. This prompted us to investigate whether there are specific changes in heterochromatin associated with interspecific hybridizations. Indeed, we found that chromatin was less condensed in the endosperm, while the embryo was not affected. Loss of chromosome condensation was connected with a strong loss of CHG and CHH methylation and mitotic abnormalities. Genome-wide sequencing of hybrid endosperm revealed that the chromosome loss was random and was likely a consequence of reduced chromatin condensation. Consistent with reduced DNA methylation in hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions. Among those deregulated genes there were many potential targets of the AGAMOUS-LIKE transcription factor PHERES1, suggesting that reduced DNA methylation allows PHERES1 to hyperactivate its targets. Since the identified QTLs were also associated with pericentromeric regions, we conclude that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.

evolutionary biology↗