Biology subjects

Tatout, C.

Publications and source records attributed to Tatout, C..

5 recordsLinked to original sources

bioRxiv2025

Replication-independent eviction of H2B.8 reveals chromatin reprogramming during seed imbibition

The transition from seed to seedling involves major changes in nuclear organization and gene expression, yet the extent to which this developmental transition requires chromatin reprogramming remains largely unexplored. Here, we report that Arabidopsis dry seed embryos accumulate the histone variant H2B.8, which contributes to higher-order chromatin organization by forming spatial clusters that structure the 3D nuclear space. H2B.8 forms heterotypic nucleosomes at euchromatic transposons and lowly expressed genes and, during imbibition, modulates the transcriptional activation of a subset of these genes. Imbibition triggers a decrease in H2B.8 transcripts and the eviction of H2B.8 proteins in a process that operates independently of DNA replication but requires protein translation and de novo transcription. Histone eviction is not limited to H2B.8 as imbibition also induces the turnover of the H3.3 histone variant, thereby initiating a broad, replication-independent chromatin reprogramming process. These findings highlight a fundamental mechanism of epigenetic regulation during early plant development.

molecular biology↗

bioRxiv2025

Sorting F. graminearum core effector candidates shows multiple fungal proteins that target the wheat cell nucleus during Fusarium Head Blight

Effectors are small molecules secreted by microbial pathogens that disrupt host basal functioning and responses during infection by targeting various plant susceptibility factors. This study reports a candidate selection approach for identifying novel, potential plant nuclear localized effectors from Fusarium graminearum secretory proteins. From a dataset of core secretory proteins conserved across several Fusarium strains, candidates were selected based on predicted nuclear localization, structural characteristics, and expression profiles during infection. Transient expression in Nicotiana benthamiana confirmed accumulation in the plant nucleus, that were further confirmed in wheat protoplasts. One of these proteins was selected for yeast two-hybrid (Y2H) screening to identify wheat protein targets, using a Fusarium-infected wheat spike cDNA library specifically generated for this study. The screening identified a high confident interaction with a nuclear-localized wheat beta-amylase 2. The structural modeling of the protein complex between beta-amylase 2 and the putative effector was used to predict interacting amino acid residues and informed a deletion analysis to disrupt the interaction. This research identifies a F. graminearum secretory core protein that interacts with a conserved wheat beta-amylase 2, showcasing a method to select pathogenicity factors conserved across multiple pathogens and host plants, with implications for developing broad-spectrum resistance strategies. HighlightThis study proposes a method based on in silico and in vivo screens to identify interacting pairs between core pathogenicity effectors localized in the nucleus and susceptibility factors in plants.

plant biology↗

bioRxiv2024

Biom3d, a modular framework to host and develop 3D segmentation methods

U-Net is a convolutional neural network model developed in 2015 and has proven to be one of the most inspiring deep-learning models for image segmentation. Numerous U-Net-based applications have since emerged, constituting a heterogeneous set of tools that illustrate the current reproducibility crisis in the deep-learning field and that remain slow to spread in application fields such as 3D bioimaging. Here we propose a solution named Biom3d, a modular deep learning framework facilitating the integration and development of novel models, metrics, or training schemes for 3D image segmentation. The development philosophy of Biom3d provides an improved code sustainability and reproducibility in line with the FAIR principles and is available as a graphical user interface and an open-source deep-learning framework to target a large community of users, from end users to deep learning developers.

bioinformatics↗

bioRxiv2023

Distinct clades of TELOMERE REPEAT BINDING transcriptional regulators interplay to regulate plant development

TELOMERE REPEAT BINDING proteins (TRBs) are plant-specific transcriptional regulators that combine two DNA-binding domains, the GH1 domain shared with H1 histones that binds to linker DNA and the Myb/SANT domain that specifically recognizes the telobox DNA binding site motif. TRB1, TRB2 and TRB3 proteins recruit the Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at target genes containing telobox motifs in their promoters to repress transcription. Here, we characterize the function of TRB4 and TRB5, which belong to a separate TRB clade conserved in spermatophytes. TRB4 and TRB5 affect the transcriptional control of several hundred genes involved in developmental responses to environmental cues, the majority of which differ from differentially regulated genes in trb1 trb2 trb3, suggesting distinct modes of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly at TSS and promoter regions of transcriptionally active and H3K4me3-marked genes but is not enriched at H3K27me3-marked gene bodies. TRB4 physically interacts with the PRC2 component CURLY LEAF (CLF), but, unexpectedly, loss of TRB4 and TRB5 partially suppresses the developmental defects of clf mutant plants, by acting as transcriptional activators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, collectively unveiling that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.

plant biology↗

bioRxiv2021

NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects

BackgroundThe three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization. ResultsWe present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allows their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest. Conclusion and availabilityNODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis. The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE.

bioinformatics↗