Biology subjects

Ducasse, A.

Publications and source records attributed to Ducasse, A..

4 recordsLinked to original sources

bioRxiv2025

Fbxl10/Kdm2b is required for Kmt2b/Mll2 binding across thegenome and regulates H3K4 methylation on bivalent promoters

The presence of histone modifications associated with both transcriptional repression (H3K27me3) and activation (H3K4me3) on key developmental promoters in embryonic stem cells results from the co-localization of repressive Polycomb group (PcG) and activating Trithorax group (TrxG) protein complexes. Functional interactions between PcG and TrxG on these promoters are not fully understood. Here we focus on the relationships between Fbxl10/Kdm2b, a component of a PcG complex PRC1, and Kmt2b/Mll2, an essential component of TrxG at bivalent promoters. Computational analysis of previously published data revealed genome-wide correlation between chromatin occupancies of these two proteins, suggesting potential crosstalk between Kdm2b and Mll2 at both active and repressed promoters. We tested this hypothesis experimentally and found that loss of Kdm2b resulted in depletion of Mll2 at promoters genome-wide, suggesting that Kdm2b is required for Mll2 occupancy at both bivalent and active promoters. Loss of Kdm2b or the core PRC1 component Ring1b also resulted in the reduction of H3K4me3 specifically at bivalent promoters. These findings provide a direct pathway for cooperation between PcG and TrxG at bivalent promoters, suggesting an unexpected modification to the current model of bivalency. In addition, these findings reveal genome-wide role of Kdm2b independent of the full PRC1 complex.

molecular biology↗

bioRxiv2024

Plant-plant interactions in wheat mixtures modulate mean and variance of susceptibility to Septoria tritici blotch

Varietal mixtures are a promising agro-ecological approach to stabilizing yields by reducing diseases. The effects of mixtures stem from modifications of epidemiological processes and plant-plant interactions, which could explain some of the paradoxical observations made in the field. However, the role of plant-plant interactions in modifying bread wheat and durum wheat susceptibility to septoria tritici blotch remains to be elucidated. Our study aimed to determine the effect of such plant-plant interactions, by producing full matrices of binary mixtures in the absence of epidemics, on septoria symptoms--specifically necroses (lesions) and pycnidia (spore-containing structures). We employed statistical modeling to compare the mean and variance of focal plants phenotype in all mixtures versus pure conditions and in each mixture versus pure condition. Our findings demonstrate significant effects of plant-plant interactions on wheat susceptibility to septoria. Notably, these interactions had specific rather than general effects, with some but not all genotypic combinations significantly influencing focal susceptibility to septoria. Furthermore, mixtures resulted in reduced necrosis with lower variance, but increased pycnidia formation. These results reinforce the need to consider specific plant-plant interactions for their contribution to trait means and variances. Better considering these interactions could improve crop management strategies that enhance disease control. HighlightWheat varietal mixtures modulate the mean and variance of septoria disease symptoms through specific plant-plant interactions. Mixtures reduce lesions and their variance but increase the formation of spore-containing bodies.

plant biology↗

bioRxiv2024

Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators

Mechanisms driving the increase of cell growth in developing leukemia are not fully understood. We focused on epigenomic regulation of this process by analyzing the changes of chromatin marks and gene expression in leukemic cell clones as they progressed towards increased proliferation in a mouse model of acute myeloid leukemia (AML). This progression was characterized by gradual modulation of chromatin states and gene expression across the genome, with a surprising preferential trend of reversing the prior changes associated with the origins of leukemia. Our analyses of this modulation in independently developing clones predicted a small set of potential growth regulators whose transcriptomic and epigenomic progression was consistent between clones and maintained both in vivo and ex vivo. We selected three of these genes as candidates (Irx5 and Plag1 as growth suppressors and Smad1 as a driver) and successfully validated their causal growth effects by overexpression in leukemic cells. Public patient data confirmed expression levels of IRX5 and SMAD1 as markers of AML status and survival, suggesting that multiomic analysis of evolving clones in a mouse model is a valuable predictive approach relevant to human AML.

molecular biology↗

bioRxiv2022

Unsuspected transcriptional regulations during rice defense response revealed by a toolbox of marker genes for rapid and extensive analysis of expression changes upon various environments

Since rice (Oryza sativa) is an important crop and the most advanced model for monocotyledonous species, acceding to its physiological status is important for many fundamental and applied purposes. Although this physiological status can be obtained by measuring the transcriptional regulation of marker genes, the tools to perform such analysis are often too expensive, non flexible or time consuming. Here we manually selected 96 genes considered as biomarkers of important processes taking place in rice leaves based on literature analysis. We monitored their transcriptional regulation under several treatments (disease, phytohormone inoculation, abiotic stress...) using Fluidigm method that allows to perform ~10 000 RT-QPCR reactions in one single run. This technique allowed us to verify a large part of known regulations but also to identify new, unsuspected regulations. Together, our set of genes, coupled to our data analysis protocol with Fluidigm brings a new opportunity to have a fast and reasonably cheap access to the physiological status of rice leaves in a high number of samples.

plant biology↗