3D genome reorganization and symbiotic nodulation (IPS2 / SPS)

Legumes establish symbiotic interactions with soil-dwelling rhizobial bacteria, leading to the formation of nitrogen-fixing root nodules. This process requires extensive transcriptional reprogramming, which is associated with dynamic changes in DNA methylation and histone modifications. However, the role of three-dimensional (3D) genome architecture in symbiosis remains largely unexplored. In a new collaborative study published in Plant Communications between the teams of Florian Frugier (SILEG) and Moussa Benhamed (ChromD) at IPS2, we revealed using High-throughput Chromosome Conformation Capture (Hi-C), that the 3D chromatin landscape undergoes major reorganizations in nitrogen-fixing symbiotic nodules compared with non-symbiotic roots and non-nitrogen-fixing nodules. These changes involve alterations in A / B compartmentalization and the establishment of enhancer-promoter loops linked to the symbiotic program. Strikingly, we identified a long-range chromatin loop bridging a 15 kb distal enhancer to the proximal promoter of the NODULE INCEPTION (NIN) gene, a master regulator of nodulation. This enhancer region contains multiple putative cytokinin (CK) response elements, and the CK-dependent induction of NIN in roots is associated with this enhancer-promoter interaction. Moreover, we demonstrated that the CK signaling transcription factor RESPONSE REGULATOR B3 (RRB3) binds specifically to this distal enhancer region and participates in forming enhancer-promoter looping. Altogether, these results uncovered a critical role for 3D chromatin reorganization in regulating gene expression during the legume-rhizobium symbiosis, highlighting a regulatory mechanism through which hormonal signaling shapes genome architecture and modulates NIN activation via long-range chromatin looping.   Contact : camille.fonouni-farde@universite-paris-saclay.fr

sciencedirect.com

Beware of misinterpretations in -omics analyses! (IPS2-SPS)

A very large proportion of false specific DEG when using few replicates and Venn Diagramms.   Omics analyses represent a crucial step in the search for condition-specific events and often rely on Venn diagrams. In stress experiments for example, the presence of differentially expressed genes exclusively under combined stress conditions is frequently interpreted as evidence of non-additive effects: the effect of combined stresses would differ from the sum of the effects of individual stresses.   In an article published in Nature Plants (Ferraro et al. 2026), to test the relevance of this line of reasoning, the Gnet team and the OGE team with several collaborators at IPS2, and the POPS, PAPPSO and Phenoscope platforms, generated a transcriptomic and proteomic dataset under a control condition, two single stresses, and the combination of both stresses, with 22 biological replicates.   Analysing this dataset, Ferraro et al. demonstrate that identifying specific responses using Venn diagrams generates many false positives. This is explained by the low statistical power inherent in most omics studies that use  too few replicates (typically around 3).   Ferraro et al. 2026 thus highlights the need to interpret any claims about the specificity of such omics datasets with caution, and advocate for improvements in statistical modeling to avoid misleading biological interpretations.   Contact : guillem.rigaill@universite-paris-saclay.fr   https://www.nature.com/articles/s41477-026-02303-x     Figure: Evolution of the number of true and false specific DEGs as a function of the number of replicates. (Left) Venn diagram of DEGs under single and combined stress conditions; (Right) Number of genes correctly identified as specific (blue), falsely identified as specific (red), and falsely identified as differentially expressed (gray) as a function of the number of replicates.

nature.com

New genomic techniques for plants to boost innovation in sustainable agriculture | News | European Parliament

Parliament has adopted new rules facilitating access to new plants that are climate and pest resistant, give higher yields and require fewer pesticides.

europarl.europa.eu

New insights into the regulation of the SNC1 resistance gene (IPS2, SPS)

To defend against pathogens (bacteria, fungi, etc.), plants have a complex immune system composed of two main lines of defense: Pattern-Triggered Immunity (PTI) triggered by the recognition of Pathogen-Associated Molecular Patterns (PAMPs) at the plasma membrane, and Effector-Triggered Immunity (ETI) triggered by the detection of microbial effectors within plant cells. Long considered independent, recent studies show that PTI and ETI interacts closely. For instance, the PAMP-induced Mitogen Activated Protein Kinases 3 and 6 (MPK3/6) are involved in the induction of certain immune genes, such as the SNC1 gene, coding for receptors of effectors. However, the underlying regulatory mechanisms remain largely unknown.   In a research article published in Scientific Reports, researchers from the STRESS team at IPS2 have shown through genetic approaches that the chromatin remodeling factor 5 (CHR5) acts downstream of MPK3/6 to promote the expression of SNC1. The authors also showed that, while CHR5 does not regulate the abundance or activity of MPK3/6, the combination of autoimmune gain-of-function mutants for MPK3 and SNC1 leads to a strong synergistic effect. Overall, the results obtained identify a new MPK3/6-CHR5-SNC1 signaling module and thus contribute to a better understanding of the links between PTI and ETI.   Contact:  julien.lang@universite-paris-saclay.fr

nature.com

Anniversaries of the M2 in Plant Sciences

The 2025-2026 academic year marked the anniversaries of the two tracks of the Master’s 2 in Plant Sciences: the Research track celebrated its 10th anniversary, and the Professional track celebrated its 25th anniversary.

master-sciences-du-vegetal.fr

Fascination of Plants Day 2026 - SPS - Home

On May 21st, nearly 60 high school students had the opportunity to participate in a special day organized by SPS in the framework of the Fascination of Plant Day 2026

eng-saclay-plant-sciences.hub.inrae.fr

https://graduate-schools-network.fr/

The Graduate School Network France, of which SPS is part, has launched its official website, where you can discover the research, mobility and collaboration activities, and the master training programs. Link: https://graduate-schools-network.fr/

graduate-schools-network.fr

Master's students' portraits - Karel Turquier

Meet our Master's students - Karel Turquier, a French student of the  M1 in Integrative Biology and Physiology – Plant Sciences, who was awarded with an SPS scholarship. 

master-sciences-du-vegetal.fr

Mobilité à Saclay – Rodrigo Fernandez - SPS - Home

From Argentina to Saclay : Rodigo Fernandez’s mobility experience "Rodrigo Fernandez and his supervisor at I2BC, Pablo Calzadilla, look back at Rodrigo’s visit to Saclay, co-funded by SPS under the call Mobility for student"

eng-saclay-plant-sciences.hub.inrae.fr

A change in the cell wall status initiates the elimination of the nucellus in Arabidopsis (IJPB, SPS)

"Seeds evolved when plants retained the female spores inside the parent tissue. The growth of the spores was accommodated by removing part of the nucellus, the maternal tissue responsible for female meiosis. Here, we demonstrate that modification of galacturonic acid polymers in the cell wall leads to nucellus cell death and eventual elimination. This work highlights the crucial contribution of extracellular polysaccharides to the development of multicellular organisms."

pubmed.ncbi.nlm.nih.gov

Master's students' portraits - Léa Dehedin

Meet our Master's students - Léa Dehedin, a French student of the  M1 in Integrative Biology and Physiology – Plant Sciences, who was awarded with an SPS scholarship. 

master-sciences-du-vegetal.fr

Publications SPS - April - SPS - Home

Find here the publications citing SPS appeared in the last month. Congrats to all the authors! 

eng-saclay-plant-sciences.hub.inrae.fr

« La brevetabilité des plantes pourrait diminuer la diversité génétique et appauvrir l’innovation » (tribune, Le Monde)

Un collectif de généticiens, d’agronomes et de biologistes alerte, dans une tribune au « Monde », sur le risque d’une monopolisation accrue des semences par quelques multinationales, ce qui serait contraire à l’objectif affiché d’une agriculture durable.

lemonde.fr

Saclay Plant Sciences (SPS), Master's students' portraits - Mamour GUEYE

Meet our Master's students - Mamour GUEYE, a Senegalese student with a Bachelor's degree in Plant Biology from the University of Angers and recipient of a Saclay Plant Sciences (S PS) scholarship, is enrolled in the M1 Integrative Biology and Physiology - Plant Sciences at the Paris-Saclay University.

master-sciences-du-vegetal.fr