Biology subjects

Kutashev, K.

Publications and source records attributed to Kutashev, K..

3 recordsLinked to original sources

bioRxiv2025

Developmentally-controlled generation of tRNA halves facilitates translational repression during sexual reproduction

The role of transfer RNAs (tRNAs) as mediators between the genetic code and protein synthesis is well established. In parallel, tRNAs can generate different types of functional small RNAs (sRNAs) that accumulate during stress and certain developmental processes across diverse organisms. Interestingly, this class of sRNAs (termed tRNA-derived sRNAs, tsRNAs) accumulate in the male gamete of mammals, insects, and plants but their role in these reproductive cells is unclear. Here, we determine the molecular pathway of tsRNA biogenesis in the plant male gamete-containing structure (the pollen grain) and identify their role in mediating the characteristic translational repression taking place in this tissue. Our data demonstrates that male-accumulating tsRNAs are generated by a cell-controlled pathway to aid in mediating reproductive translational repression and that their accumulation is key to ensuring the proper function of the pollen grain.

plant biology↗

bioRxiv2024

Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections

Single-molecule fluorescence in situ hybridization (smFISH) has emerged as a powerful tool to study gene expression dynamics with unparalleled precision and spatial resolution in a variety of biological systems. Recent advancements have expanded its application to encompass plant studies, yet a demand persists for a simple and robust smFISH method adapted to plant tissue sections. Here, we present an optimized smFISH protocol (cryo-smFISH) for visualizing and quantifying single mRNA molecules in plant tissue cryosections. This method exhibits remarkable sensitivity, capable of detecting low-expression transcripts, including long non-coding RNAs. Integrating a deep learning-based algorithm in our image analysis pipeline, our method enables us to assign RNA abundance precisely in nuclear and cytoplasmic compartments. Compatibility with Immunofluorescence also allows RNA and endogenous proteins to be visualized and quantified simultaneously. Finally, this study presents for the first time the use of smFISH for single-cell RNA sequencing (scRNA-seq) validation in plants. By extending the smFISH method to plant cryosections, an even broader community of plant scientists will be able to exploit the multiple potentials of quantitative transcript analysis at cellular and subcellular resolutions.

cell biology↗

bioRxiv2024

Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types

O_LIThroughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adjust to the changing environment that can elicit varying amounts of DNA damage. C_LIO_LIUsing a combination of state-of-the-art cell biology methods including whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH), allowing detection of individual mRNA molecules in intact plant tissue and plant cell cycle reporter lines we investigated how the transcriptional activation of a key homologous recombination (HR) gene, RAD51, occurs in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. C_LIO_LIThe results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. C_LIO_LIThis work advances the current comprehension of DNA damage response in plants showing quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants. C_LI

plant biology↗