Biology subjects

Cermak, V.

Publications and source records attributed to Cermak, V..

4 recordsLinked to original sources

bioRxiv2026

Imprinted regulatory networks reveal the molecular cross-talk between paternal and maternal genomes in the endosperm of Arabidopsis arenosa

Summary paragraphImprinted genes do not act alone to shape seed development, but as a complex network -- just like any other gene. Yet, the molecular context in which they are embedded, i.e. their gene network, remains largely understudied. To address this knowledge gap, we characterized the imprintome of Arabidopsis arenosa at the species-level and used gene regulatory network analyses. We show that genomic imprinting preferentially affects only a few pathways, offering candidates for dosage sensitive processes and the molecular arena of parental conflict. In these pathways, some imprinted genes act as hub genes, among which NRPE1, highlighting the importance of epigenetics in endosperm development. The interaction between parental genomes was rather one-sided: paternally expressed regulators preferentially targeted PEGs, while maternally expressed regulators targeted both PEGs and MEGs indiscriminately. This aligns with a self-promoting paternal influence and a maternal buffer under a parental conflict scenario. Shared paternal and maternal regulation of downstream targets was nevertheless common, and we reveal novel molecular interactions between imprinted regulators. Overall, our work shows how genomic imprinting may act as a molecular means for parental conflict, but also highlights the importance of parental molecular coordination in endosperm development.

plant biology↗

bioRxiv2026

Transcriptomic insights into triploid seed failure in Arabidopsis arenosa natural populations

O_LIPolyploidy is a key evolutionary force in plants; among its many consequences, hybridization between diploids and polyploids is restricted due to the "triploid block". While the molecular mechanisms of this postzygotic barrier are extensively studied in the model species Arabidopsis thaliana, our understanding of the triploid block in natural systems remains limited. C_LIO_LIHere, we investigated the transcriptome of failing triploid seeds in Arabidopsis arenosa, a close relative of A. thaliana with diploid and autotetraploid populations meeting in nature. We also identified A. arenosa imprinted genes. C_LIO_LITriploid seeds showed preferential misregulation of imprinted genes, which parallels the parent-of-origin features of the triploid block. Tissue-specific transcriptomic analyses revealed pathogen defense-like response being recurrently affected in the endosperm and seed coat. This pathway is commonly misregulated in all species with triploid seed transcriptomes studied to date. The associated genes however are likely more involved in cell-cell signaling rather than pathogen defense per se. C_LIO_LIAltogether, this study depicts a thorough molecular landscape of the triploid block for the first time in natural systems. Combining data on the understudied maternal excess transcriptome, a new imprintome, a tissue-specific focus, and a cross-species comparison, this study also advances our understanding of the triploid block and seed development. C_LI

evolutionary biology↗

bioRxiv2026

Transcription elongation factor SPT6L recruits ARGONAUTE to guide mRNA cytosine methylation preventing premature termination in plants

In plants, an essential component of the RNA Polymerase II (Pol II) complex, SPT6L, contains a unique C-terminal ARGONAUTE binding domain - AGO-hook. Although it has been recently shown that SPT6L is also part of the Pol V complex, where its AGO-hook might participate in the RNA-directed DNA methylation pathway, several lines of evidence suggest that the AGO-hook should also have a function in the Pol II complex. Here we demonstrate that in Arabidopsis thaliana, SPT6L recruits AGO4 via the AGO-hook domain, independently of Pol V. Using direct RNA sequencing, we show that this interaction is connected with guided deposition of 5-methylcytosine (m5C) on Pol II transcripts. The role of AGO4 in m5C guidance was further supported by increased methylation of GFP transcripts after their targeting by sRNAs in tobacco BY-2 cells. Removing the SPT6L AGO-hook (spt6l{Delta}Ah) in A. thaliana resulted in the hypomethylation of specific m5C sites, mimicking even stronger RNA hypomethylation observed in the ago4 mutant. Native elongating transcript sequencing revealed that impaired targeting of m5C methylation in the spt6l{Delta}Ah mutant was accompanied by Pol II stalling downstream of hypomethylated cytosines. Furthermore, this stalling appeared to be associated with premature transcription termination, which we also detected in published transcriptomes of mutants lacking AGO4, as well as TRM4B that is the major RNA m5C methyltransferase. Our findings uncover a novel "guide-and-modify" mechanism in which SPT6L integrates sRNA-directed epitranscriptomic marking with transcription elongation, ensuring proper mRNA termination.

plant biology↗

bioRxiv2024

SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway

RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naive loci by interconnecting Pol II and Pol V activities.

plant biology↗