I2BC Paris-Saclay

From DNA sequencing and studies of genome function and organization—covering viruses, bacteria, archaea and eucaryotes, this collective book explores genomes and their role in life, evolution, and diversity.

A collective book that traces the history of genetics and the major discoveries surrounding genomes. The genome, the complete set of genetic information, builds, operates, and reproduces all living beings, serving as the engine of their evolution. Thanks to DNA, genetic information is stored, decoded, duplicated, and transmitted. But the study of the genome goes much further: it allows us to understand life, trace the history of species, and identify non-coding DNA regions that are nonetheless essential for life, the protection of genetic material, and its diversity. From DNA sequencing and genome function to the mechanisms of evolution—covering viruses, bacteria, archaea and eucaryotes, —the book explores how scientists today are striving to understand genome function and evolution.

Coordinated by Frédéric Boccard, Director of the I2BC, this book brings together chapters written by several French scientists, including Mireille Bétermier, Group Leader at the I2BC.

More information: https://www.cnrseditions.fr/catalogue/biologie-et-sante/genomes/

Contact: Frédéric Boccard frederic.boccard@i2bc.paris-saclay.fr

Master Unix for bioinformatics with a free, progressive skills sheet and interactive Sandbox.bio tutorials—no install needed! Check it out here: https://sandboxbio.france-bioinformatique.fr/

As data generation in life and health sciences accelerates, mastering core bioinformatics skills—especially Unix command-line proficiency—has become essential. In response, the e-learning working group of the IFB (Institut Français de Bioinformatique), in which Claire Toffano-Nioche from the BIOI2 facility of I2BC participates, developed a progressive Unix skill sheet tailored for life scientists with little or no prior experience, recently published in PLoS Comput Biol. This skills sheet summarises the most commonly used Unix commands in the field of bioinformatics. Skills are organised according to increasing levels of difficulty and thematic groups and are cumulative, meaning that skills acquired at a given level are required at the next level. Each skill has been defined operationally by following Bloom's taxonomy of learning objectives. This framework can be freely reused (CC BY 4.0) - by learners as well as tutors - and serves as inspiration for defining the competencies or prerequisites of a training course, or for evaluating the level of a student.

Following this sheet, the e-learning working group directly implemented progressive, interactive sessions that can be used for self-paced learning or in classroom settings. These sessions are deployed via Sandbox.bio, an open-source platform leveraging WASM (WebAssembly) technology. This ensures seamless access from any browser—no installation required—while enabling computations to run locally on the user’s machine.

To further support self-paced learning, BIOI2 also offers autotraining course materials on their website (https://bioi2.i2bc.paris-saclay.fr/training). These resources draw inspiration from—and contribute back to—multiple open courses, including those from the IFB, creating a collaborative cycle of shared knowledge and continuous improvement.

More information:

• Link towards the article: https://doi.org/10.1371/journal.pcbi.1014133
• Link towards sandboxbio IFB: https://sandboxbio.france-bioinformatique.fr/
• Link towards the skill sheet: https://zenodo.org/records/18686109
• Link towards BIOI2 training page: https://bioi2.i2bc.paris-saclay.fr/training/

Contact: contact-bioi2@i2bc.paris-saclay.fr

The numerous tiny germline chromosomes of Paramecia end in DNA segments produced over evolutionary time by the activity of Helitron mobile elements. These chromosome ends are eliminated during development of the individual by a novel mechanism.

Many eukaryotes are able to eliminate chromosome segments or even entire chromosomes during somatic differenciation. This programmed DNA elimination process illustrates eukaryotic genome plasticity and raises questions about the underlying molecular mechanisms. Among the unicellular ciliated protozoans, which include paramecia, the somatic and germline fonctions of chromosomes are separated in two distinct nuclei.

The diploid germline nucleus (MIC, ~ 100 Mb in Paramecium) undergoes meiosis and transmits the genetic information between generations. The polyploid somatic nucleus (MAC, ~ 70 Mb) is responsible for gene expression, but is destroyed at each generation, when a new MAC develops from a copy of the MIC.
Identification of the sequences that undergo programmed DNA elimination requires knowledge of the MIC genome sequence. More than 10 years of research involving several University Paris-Saclay teams and platforms has provided chromosome-scale assemblies of MIC DNA for 7 members of the Paramecium aurelia
species complex and a telomere-to-telomere assembly for one of them, P. tetraurelia. The authors show that the MIC genome consists of around 160 tiny chromosomes (300 kb – 1.2 Mb) with the highest meiotic recombination rate ever reported (420 cM/Mb). The assembly revealed that the germline chromosome ends
are eliminated very early during MAC development by a  echanism different from that known to be involved in elimination of other sequences. This terminal genomic compartment contains a new clade of transposable elements (TE) that belong to the Helitron superfamily. These TE are very ancient (having diverged from other Helitron-like elements at the base of the eukaryotic tree) but have remained active in Paramecia. They appear to preferentially insert into telomeric repeats. One exciting perspective of the study is the elucidation of a novel DNA elimination pathway.

Contact: linda.sperling@i2bc.paris-saclay.fr & olivier.arnaiz@i2bc.paris-saclay.fr 

More information: https://link.springer.com/article/10.1186/s12915-026-02584-w

New discovery: a dynamic interplay between axis proteins and cohesins ensures chromosome stability during meiosis in Sordaria.

Faithful chromosome segregation during meiosis requires the coordinated action of cohesin complexes and chromosome axis proteins. How these factors interact and communicate along chromosome axes, especially during meiotic prophase I, remains however, only partially understood. Researchers of the Genome Biology Department of the I2BC investigated the functional interplay between the cohesin components and regulators (Rad21, Rec8, Wapl, Sororin, Spo76/Pds5) and two meiosis-specific axis proteins Red1 and Hop1. Analysis of multiple combinations of their corresponding null mutants and of their genetic-epistasis interactions in the fungus Sordaria macrospora revealed a hierarchical regulatory network for their recruitment and releasing. Their work uncovers an unexpected role of axis proteins Red1 and Hop1, that together with Sororin, provide stage-specific protection of Spo76/Pds5 against Wapl-mediated release. Furthermore, we identify that Spo76/Pds5 is the main target of Wapl and acts as a central guardian of kleisin stability against Slx8/STUbL-dependent proteasomal degradation.

Together, these findings show that a dynamic crosstalk between axis proteins and cohesins is crucial to preserve axis integrity and to ensure accurate meiotic progression.

More information: https://doi.org/10.1371/journal.pgen.1012001

Contact: Stéphanie BOISNARD stephanie.boisnard@i2bc.paris-saclay.fr

Using functional genomics in sorted Salmonella populations and high-resolution microscopy, the researchers of the I2BC show that the expression of Pathogenicity Island 1 is associated with chromatin remodeling and with the repositioning of this region toward the nucleoid periphery.

Chromatin provides a universal framework for organizing and regulating genomes across the three domains of life. In bacteria, it is composed of intrinsically supercoiled DNA associated with small DNA-binding proteins known as nucleoid-associated proteins (NAPs). Their binding can induce DNA bending, bridging, coating, and/or wrapping, giving rise to distinct modes of chromatin organization.
Bacterial chromatin can exist in a repressed state (silent chromatin) or in an actively transcribed state (active chromatin). Silent chromatin is largely associated with H-NS, a xenogeneic silencer that restricts the costly expression of genes acquired by horizontal transfer. In contrast, active chromatin is densely occupied by RNA polymerase and is characterized by different levels of DNA supercoiling. However, the changes in protein occupancy and chromatin organization that accompany transitions between these two states remain poorly understood.
Researchers of the Genome Biology Department of the I2BC in collaboration with the NGS and the Imaging facility of the I2BC and the Trinity College Dublin (Ireland), have unveiled the chromatin organization of horizontally acquired regions in Salmonella enterica serovar Typhimurium, which are essential for its pathogenicity. They show that expression of Pathogenicity Island 1 (SPI-1) is accompanied by local chromatin remodeling, marked by profound changes in three-dimensional organization and protein occupancy. This remodeling is also associated with the repositioning of SPI-1 toward the nucleoid periphery.
These findings provide new insights into the interplay between xenogeneic silencing, counter-silencing mechanisms, chromatin architecture, and the evolutionary integration of acquired DNA. They also reveal a finely tuned chromatin remodeling process that minimizes the cellular cost of activating pathogenicity islands, and they establish a direct link between the linear (1D) organization of the genome and its three-dimensional (3D) folding.

More information: https://www.nature.com/articles/s41467-025-67746-w

https://www.insb.cnrs.fr/fr/cnrsinfo/comment-les-genes-de-virulence-reorganisent-le-genome-de-salmonella-0

Contact: Vicky Lioy virginia.lioy@i2bc.paris-saclay.fr

A new ED-TA method which enabled genomics investigation of plasmid establishment during conjugative transfer was developed by I2BC researchers. They showed robust induction of a subset of plasmid genes at the early stages of conjugation through single-stranded DNA promoters.

Bacterial conjugation is a principal mode of horizontal gene transfer which has important life science implications including bacterial genome evolution, dissemination of genetic traits and bioengineering applications. Notably, the spread of multidrug resistance via conjugative plasmids is one of the biggest concerns in global public health. Although conjugation has been studied since 1940s and the overall procedure is widely known and well documented, molecular details of reactions that establishes a transferred plasmid in the new host cell remain elusive. In addition, there are specific regulatory mechanisms for temporal expression of plasmid genes, that are also crucial for successful conjugation as they allow timely expression and function of plasmid-encoded arsenal against host defense mechanisms.

Genomics-based studies of plasmid establishment were previously hampered by the nature of conjugation which takes place within a mixture of cell populations. Essentially, they require the separation of subpopulations before the DNA/RNA extraction to avoid contamination of indistinguishable plasmid DNA/RNA from the donor. Researchers of the Genome Biology Department of the I2BC, described the development of a new method, called ED-TA, which exploits a donor mutant hypersensitive to hypoosmotic shock. ED-TA allows unprecedently quick and efficient « Elimination of Donor population for Transconjugant Analysis». Using a clinically relevant model multidrug resistant conjugative plasmid, pESBL, they elucidated its transcription profile in successful and abortive conjugation. Researchers also showed single-stranded DNA promoters allow robust induction of a subset of genes at the early stages of conjugation. As the ED-TA method is straightforward and broadly applicable, further research taking advantage of the method will shed light on important molecular mechanisms of plasmid establishment after conjugation.

More information: doi.org/10.1093/nar/gkaf1299

https://www.insb.cnrs.fr/fr/cnrsinfo/une-nouvelle-methode-pour-suivre-de-pres-la-transmission-des-genes-chez-les-bacteries

Contact: Yoshiharu Yamaichi yoshiharu.yamaichi@i2bc.paris-saclay.fr

Cécile Courret, CNRS Researcher and recipient of an ATIP-Avenir grant, has joined the Department of Genome Biology to establish her team ‘Intragenomic Conflict and Evolution’.

Cécile's research focus on genetic conflicts and their impact on genome evolution. The basic principles of Mendelian inheritance state that in heterozygous individuals, two alleles have equal chances of being transmitted to the next generation. However, some genetic elements do not follow these rules. These so-called selfish genetic elements, such as transposons or meiotic drivers, bias inheritance in their own favor, often at the expense of the organism.

Because they disrupt essential processes like meiosis, heterochromatin regulation, and cell division, selfish elements create a persistent conflict with the host genome. This conflict triggers an evolutionary “arms race,” in which genomes evolve defense mechanisms to counterbalance the harmful effects of these elements. Far from being rare exceptions, such conflicts are now recognized as a major force shaping genome structure and function.

My research relies on the Drosophila model and combines genomic, molecular, and cytological approaches to investigate both how selfish elements perturb fundamental biological processes and how organisms respond to mitigate these disruptions. By studying systems where these conflicts are still active in natural populations, as well as the genomic signatures left by past events, Cécile's team aims to better understand how conflicts drive evolutionary innovation and shed light on the molecular basis of essential biological mechanisms.

Contact: Cécile Courret, cecile.courret@i2bc.paris-saclay.fr

The expansion of PolX DNA polymerases in the ciliate Paramecium tetraurelia has favored the functional diversification of a subset of these enzymes, with enhanced nuclear localization in DNA repair foci during programmed DNA elimination.

During its sexual cycle, Paramecium massively rearranges its genome by removing tens of thousands of internal eliminated sequences (IESs) from its developing somatic nucleus. This process involves the introduction of programmed DNA double-strand breaks (DSBs), followed by efficient DSB repair using the non-homologous end joining (NHEJ) pathway. In this system, DSB repair requires not only the core NHEJ factors Ku70/80 and Xrcc4/Lig4, but also additional enzymes that accurately process the 4-base 5′-overhangs of the broken DNA ends created at IES excision sites.

In this study, we identify four orthologs of human DNA polymerase lambda in P. tetraurelia —PolXa, PolXb, PolXc, and PolXd— as key players in repairing IES excision junctions. Cells lacking these PolX enzymes accumulate genome-wide DNA damage, including unrepaired double-strand breaks, small deletions, and retained IESs. All four PolX proteins can process DNA ends, but PolXa and PolXb are specifically produced during programmed genome rearrangement and possess a unique internal linker region that enhances their nuclear localization.

In contrast to PolXc, we show that PolXa concentrates in nuclear foci along with core NHEJ factors and a Dicer-like enzyme involved in producing IES-specific small RNAs that regulate IES excision. We propose that these foci are the sites where excised IESs are ligated into concatemers, which serve as templates for small RNA production, linking DNA repair to RNA-mediated regulation of genome dynamics.

More information: https://academic.oup.com/nar/article/53/7/gkaf286/8113560

Contact: Mireille Bétermier mireille.betermier@i2bc-paris-saclay.fr, Julien Bischerour julien.bischerour@i2bc.paris-saclay.fr 

This study uncovers a fission yeast small nucleolar RNA (snoRNA) that guides ribosomal RNA 2’- O-methylation and modulates the activities of RNA-binding proteins involved in gametogenesis, expanding our vision of the non-canonical functions exerted by snoRNAs.

Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. In a collaborative work with the I2BC B3S department and NGS facility, the epiRNA-Seq facility in Nancy and the Palancade lab at the Institut Jacques Monod, we have identified a conserved, previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in the fission yeast long non-coding RNA mamRNA and carrying two independent cellular functions. On the one hand, snR107 guides site-specific 25S rRNA 2’-O-methylation and promotes pre-rRNA processing and 60S subunit biogenesis. On the other hand, snR107 associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinct cis-motifs within snR107, including a conserved 2’-O-methylation guiding sequence. Together, our results position snR107 as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.

More Information: https://www.nature.com/articles/s41467-025-58664-y

Contact: Mathieu Rougemaille mathieu.rougemaille@i2bc.paris-saclay.fr

Researchers at the I2BC and the Ecole Normale Supérieure found that the borders that create separation between functional domains in our chromosomes have an unexpectedly large influence on those domains themselves.

Chromosomes in humans and other mammals are subdivided into “functional neighborhoods” that guide the fidelity of biological processes, including gene regulation and DNA repair. Perturbations of these neighborhoods, resulting in the fusion of adjacent domains, can lead to a variety of diseases, including cancer and developmental disorders.
In a study published in PNAS (Proceedings of the National Academy of Sciences of the USA), scientists from the Noordermeer group at the I2BC, together with their colleagues at the Ecole Normale Supérieure in Paris, report how chromosomal border elements influence the organization of the adjacent functional neighborhoods. By combining genomics-based analysis and biophysical simulations of chromosome structure, they find that the size of these borders is highly diverse, from simple “points” on the chromosome to highly extended zones of transition between neighborhoods. Computer simulations of chromosome behavior of different types of borders in-between revealed an unexpected and far-reaching impact of the borders on their neighboring domains. Rather than creating a static separation, the borders will actively influence the degree of neighborhood mixing due to a previously unrecognized mechanism whereby the borders reel-in the adjacent neighborhoods. At narrow borders, this actively promotes mixing and may cause interference between biological activity on both side of the border. Extended borders buffer against this mechanism by adding additional separation. Border structure can thus constitute a new regulatory layer in the genome to fine-tune biological processes.

More information: https://www.pnas.org/doi/10.1073/pnas.2413112122

Contact: Daan Noordermeer daan.noordermeer@i2bc.paris-saclay.fr

The translatome of HIV-1 reveals tens of alternative open reading frames (ARF), encoding conserved viral antigens. In vivo, ARF-derived peptides elicit potent HIV-specific poly-functional T cell responses mediated by both CD4+ and CD8+ T cells.

T lymphocytes play a pivotal role in controlling human immunodeficiency virus type 1 (HIV-1) infection. Their activation relies on the recognition of viral peptides, or antigens, presented on the surface of infected cells by major histocompatibility complex (MHC) molecules. It is widely assumed that these antigens arise solely from canonical HIV proteins.

Previously, we showed that HIV-specific T lymphocytes can also target peptides derived from HIV alternative reading frames (ARFs) presented by MHC molecules. However, evidence for ARFs in the HIV genome had thus far been indirect. In this new study, using ribosome profiling (RiboSeq), we identified the complete HIV-1 translatome in infected CD4⁺ T cells. This approach systematically identified virally encoded mRNA sequences actively translated in HIV-infected cells. We found that the HIV-1 genome contains over one hundred ARFs located either in the 5ʹ untranslated region (5ʹUTR) of classical viral genes or overlapping canonical HIV open reading frames.

Using two complementary methods: (1) detecting T lymphocytes specific to ARF-derived peptides in PBMCs from people living with HIV and (2) directly isolating ARF-derived peptides bound to MHC molecules via mass spectrometry–based immunopeptidomics—we demonstrate that HIV ARFs encode novel viral antigens capable of eliciting broad and potent T-cell responses. Our results expand the range of HIV antigens that could be harnessed for vaccine development and may also reveal the existence of microproteins or pseudogenes in the HIV genome.
These findings stem from the work of two complementary teams at I2BC: one led by Olivier Namy, a specialist in protein translation, and the other led by Arnaud Moris, an expert in the immune response to HIV. This collaboration also involved French research and clinical teams and the University of Tübingen in Germany.

More information: https://doi.org/10.1038/s41467-025-56773-2

Contact: Arnaud Moris arnaud.moris@i2bc.paris-saclay.fr & Olivier Namy olivier.namy@i2bc.paris-saclay.fr

Image: Sonhita Chakraborty 

The Apicomplexa-specific ACDC domain adopts a never before seen protein fold.

In collaboration with the Nessler team at the I2BC and the Llinás lab at PSU, US, we reveal that the ACDC domain, only found in DNA-binding proteins of the Apicomplexa phylum, grouping several important human pathogens including malaria, has a never before seen protein fold. We also identify potential ligands that may be optimized in the future as protein inhibitors.

More information:https://journals.iucr.org/paper?S2059798324012518

Conatct: Joana SANTOS joana.santos@i2bc.paris-saclay.fr

Ribosome remodeling drives cancer cell transformation: A single protein, RPL36A, triggers EMT.

Epithelial-mesenchymal transition (EMT) is a biological process whereby a cell loses its usual characteristics to acquire properties allowing it to move. EMT is involved in embryo formation and tissue repair in adults. However, when altered, EMT contributes to the formation of fibrosis or, in the case of a tumor cell, to the formation of metastases. In cancers, this change is comparable to a cellular metamorphosis that allows cancer cells to become more aggressive and resistant to treatments. EMT is therefore a key player in tumor progression.
EMT is extensively studied at the molecular and cellular levels because a better understanding of this process will enable the development of new therapeutic approaches. However, the translational changes that occur during EMT have so far been very poorly studied.
In this work, we have identified that the overexpression of a single ribosomal protein, called RPL36A, is sufficient to induce EMT. We have also highlighted the various translational changes that occur during EMT.
Our work reveals the importance of ribosome remodeling itself in finely modulating translation during the change in cellular identity that occurs during EMT.

More information : https://www.pnas.org/doi/10.1073/pnas.2408114121 ; In French: https://www.insb.cnrs.fr/fr/cnrsinfo/des-modifications-de-la-composition-du-ribosome-accompagnent-les-changements.

Contact: Olivier NAMY olivier.namy@i2bc.paris-saclay.fr

A condensin I complex, known for shaping chromosome organization in eukaryotes, is essential to DNA elimination in Paramecium

During development, many organisms eliminate specific germline DNA sequences to shape their somatic genome. But how do cells target which sequences to remove? The team “Programmed Genome Rearrangements” has addressed this question in the ciliate Paramecium tetraurelia. Because of its nuclear dimorphism, this unicellular eukaryote provides a powerful model to study somatic differentiation at the genomic scale. At each sexual cycle, a new somatic macronucleus (MAC), specialized for gene expression, is formed from a copy of the germline micronucleus (MIC), inherited from the previous generation. This process involves the elimination of one third of germline sequences, including transposable elements and satellite DNA, to ensure proper gene function and progeny survival.

In collaboration with scientists from the Institut Jacques Monod, the authors have uncovered a surprising new role for a development-specific condensin I, a complex from the SMC family (Structural Maintenance of Chromosomes) generally known for organizing chromosomes in three dimensions. Using TurboID and protein co-immunoprecipitation, combined with quantitative mass spectrometry, we found that the developmental condensin I complex interacts with the PiggyMac (Pgm) endonuclease, an enzyme essential for cutting and removing specific germline DNA sequences during MAC development. High-throughput sequencing of the DNA extracted from purified new MACs revealed that when cells are depleted of condensin I, the germline genetic material is massively retained in the somatic genome. This demonstrates that condensin I plays a key part in programmed DNA elimination.

This discovery suggests that 3D genome organization may help target which sequences are removed. The condensin complex localizes to the developing new MAC, where it stabilizes Pgm and its partners. However, the exact level at which spatial genome architecture influences PDE remains an open question.

More info: https://doi.org/10.1093/nar/gkag351

Conatct: Mireille Bétermier mireille.betermier@i2bc.paris-saclay.fr

Researchers from the I2BC recently visited Collège A. Fournier in Orsay to introduce students to various scientific career paths. Magali Noiray presented the institute’s state-of-the-art facilities, while Olivier Namy showcased the exciting work of its research teams.

Science is for everyone, and the journey can start at any age. Let’s inspire the next generation of innovators!

More information about I2BC: https://www.i2bc.paris-saclay.fr/ 

A great thanks to Magali & Olivier for their time and commitment!

Noncoding DNA can generate microproteins, some of which evolve into new genes. We show that de novo genes preferentially originate from GC-rich, foldable sequences, revealing how base composition channels the birth of new proteins.

Noncoding regions of eukaryotic genomes are widely transcribed and constitute a major source of novel microproteins, some of which eventually become fixed as de novo genes - a process known as de novo gene birth that plays a significant role in species adaptation. However, the structural properties of these nascent proteins and the factors governing their evolutionary fate remain poorly understood. In particular, the role of genome nucleotide composition (GC content) in shaping their biophysical properties has remained unclear. In this study, researchers of the I2BC, analyzed the foldability and sequence properties of millions of putative microproteins encoded by intergenic open reading frames (ORFs) from 3,379 eukaryotic species spanning a broad range of GC contents (18–79%). Results show that GC content strongly influences amino-acid composition and structural tendencies, suggesting distinct cellular impacts if non-genic regions are pervasively expressed. AT-rich species predominantly encode ORFs biased toward hydrophobic, aggregation-prone sequences, whereas GC-rich species tend to encode more hydrophilic, disorder-prone ORFs. ORFs from genomes with intermediate GC content display a more balanced composition and higher folding potential, with many expected to adopt proto-folds. To assess how these properties relate to gene emergence,the authors traced the evolutionary history of several hundred de novo proteins across 22 species using phylostratigraphy, targeted de novo gene searches, and ancestral sequence reconstruction. Researchers find that de novo genes preferentially originate from GC-rich ORFs with intrinsic folding potential. Together, our results reveal that the interplay between GC content and foldability - rooted in the structure of the genetic code - shapes the emergence of novel genes.

More information: https://www.nature.com/articles/s41467-025-68022-7

Contact: Anne Lopes anne.lopes@i2bc.paris-saclay.fr

Understanding how the essential complexes —the coregulator Mediator and the chromatin remodeling complex RSC/PBAF— cooperate in the nucleus

In eukaryotes, transcription and DNA repair occur in the crowded context of chromatin. Dysfunctions of these processes can lead to cancers. Mediator is an essential and conserved multisubunit coactivator complex, mutated in many cancers. However, it remains largely unknown how Mediator and chromatin regulators coordinate their functions. A recent publication of the team suggests the novel hypothesis that Mediator acts in conjunction with the chromatin remodeling complex RSC (Remodels the Structure of Chromatin) of SWI/SNF family, homologous to PBAF (Polybromo-associated BAF) in human, representing the most frequently mutated complexes in cancers. Building on this recent publication, a new project has been supported by Ligue Nationale contre le cancer. Using the yeast model, with a perspective to extend the study to human cells, the team intends to decipher the molecular mechanisms involved in functional cooperation between these essential coregulator complexes in transcription regulation, DNA repair and chromatin organization relevant for cancer biology.

Contact: Julie Soutourina julie.soutourina@i2bc.paris-saclay.fr

Funded by the European Research Council (ERC synergy 2025), the project “3Stops2Go” leaps over the “three red lights” of premature stop codons to re-express critical protein and correct genetic diseases.

The project, recently funded by an ERC Synergy Grant 2025, aims to target premature termination codon (PTC)mutations, which prematurely halt protein translation and are involved in about 11% of human genetic diseases.
By combining expertise in protist biology, RNA biology, and gene therapy, the consortium of four researchers (Leoš Valášek (Institute of Microbiology, Czech Academy of Sciences, Czech Republic), Julius Lukeš (Biology Centre, Czech Academy of Sciences, Czech Republic), Olivier Namy (Université Paris-Saclay, CEA, CNRS, France / I2BC, France), and Mark Osborn (University of Minnesota, USA)) aims to harness natural stop-codon bypass mechanisms to develop therapeutic tools (engineered tRNAs and readthrough inducers), test them in patient-derived cells and animal models, and ultimately pave the way toward clinical applications.

More information: https://erc.europa.eu/news-events/news/synergy-grants-2025-examples-projects

Contact: Olivier Namy olivier.namy@i2bc.paris-saclay.fr>

The Ribosome Quality Complex protein 2 is a major player in peptide release from stalled ribosomes.

Cells employ many quality control mechanisms during protein biosynthesis. Defects impairing messenger RNA decoding can cause ribosomes to stall, thereby distorting gene expression. Ribosome stalling results in ribosomes being sequestered in an inactive state on mRNA and represents a challenge for both ribosome homeostasis and cell survival. Eukaryotic cells prevent the accumulation of potentially toxic aberrant polypeptides and maintain ribosome availability by employing surveillance and clearance mechanisms, including the evolutionarily conserved ribosome-associated quality control complex (RQC). The rescue pathways dissociate the stalled ribosome, leading to the release of a 40S subunit attached to the mRNA and a 60S subunit still attached to a tRNA with the elongating peptide. RQC mediates the ubiquitination, extraction, and rapid degradation of the aberrant nascent peptide. In particular, Rqc2p recruits charged alanyl- and threonyl-tRNAs at the same position as an A-site tRNA, resulting in C-terminal extensions composed of alanine and threonine residues (CAT tails). These CAT tails may expose potential tunnel-embedded lysine residues for ubiquitination by the E3 ligase Ltn1. Using a genetic screen, we identified a mutant allele of RQC2 as involved in peptide release from stalled ribosomes. We characterized the mutant protein both biochemically and structurally, in collaboration with Reynald Gillet’s team (IGDR, Rennes University). We determining how the underlying point mutation reduced tRNA recruitment to the A site, thereby limiting CAT tail formation. These findings provide further mechanistic insight into the role of Rqc2p in ribosome rescue and the maintenance of ribosome homeostasis.

More Information:https://pubmed.ncbi.nlm.nih.gov/40187343/

Contact: Céline Fabret celine.fabret@i2bc.paris-saclay.fr

DNA duplication of the genetic material is a crucial step of cell proliferation. The study reveals that this step comprises two opposed strategies, coordinated by the enzyme Plk1.

In vertebrates, DNA replication involves the activation of thousands of starting points for DNA copying, known as “origins of replication”. These points are irregularly scattered across the genome. However, the precise mechanisms controlling the coordinated activation of these starting points and the regulation of the rate at which DNA is copied remain poorly understood. Any dysfunction can lead to genetic abnormalities and promote the development of cancers.
The scientists studied DNA replication using cell-free extracts from the eggs of the amphibian Xenopus laevis. This model is quite similar to replication in human cells, and has made it possible to develop a new method for analyzing the distribution of replication starting points (initiations) and the speed of replication in individualized DNA molecules. Combining this analysis with kinetic models, the scientists discovered that DNA replication relies on two dynamic and opposing strategies:
A fast strategy: high replication speed, but with fewer starting points.
A slow strategy: a slower replication speed compensated by the activation of numerous starting points.
In this context, the scientists determined that the enzyme Polo-like kinase 1 (Plk1) played a key role in coordinating these two strategies. Plk1, frequently mutated in many cancers, regulates this balance, opening up new perspectives on the control of replication and its implications in oncology. (published by Paris-Saclay and CNRS Biologie Actu (https://www.insb.cnrs.fr/fr/cnrsinfo/yin-yang-dans-la-duplication-des-chromosomes )

More Information: https://doi.org/10.1093/nar/gkaf007

Contact: Arach Goldar arach.goldar@i2bc.paris-saclay.fr Kathrin Marheineke kathrin.marheineke@ijm.fr

This study sheds light on an alternative mode of Transposable Element silencing associated with H3K27me3 instead of DNA methylation in flowering plants; it also indicates dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.

The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.
In this study, the team of Angélique Déléris showed that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerated relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. The authors also showed that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs—which we refer to as “bifrons”—that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan.
Overall, this study shedded light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.

More Information: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03466-6

Contact: Angélique Déléris angelique.deleris@i2bc.apris-saclay.fr

A large genomic region in Podospora anserina remains entirely devoid of crossovers, despite being fully colinear.

Recombination is advantageous over the long-term, as it allows efficient selection and purging deleterious mutations. Nevertheless, recombination suppression has repeatedly evolved in sex chromosomes. In fungi, sexual compatibility is driven by a locus called mating-type (mat), around which recombination suppression is also often observed.
The evolutionary causes for recombination suppression and the proximal mechanisms preventing crossing overs are poorly understood. Several hypotheses have recently been suggested based on theoretical models, and in particular, that divergence could accumulate neutrally around a sex-determining region and reduce recombination rates, a self-reinforcing process that could foster progressive extension of recombination suppression.
We used the ascomycete fungus Podospora anserina for investigating these questions: a 0.8 Mbp region around its mat locus is non-recombining (called MAT-proximal region), despite being collinear between the two mating types. This fungus is mostly selfing, resulting in highly homozygous individuals, except in the non-recombining region around the mating-type locus that displays differentiation between mating types. Here, we test the hypothesis that sequence divergence alone is responsible for recombination cessation. We replaced one mat idiomorph by the sequence of the other, to obtain compatible strains isogenic in the MAT-proximal region. Crosses showed that recombination was still suppressed in that context, indicating that other proximal mechanisms than inversions or mere sequence divergence are responsible for recombination suppression in this fungus.
This finding suggests that selective mechanisms likely acted for suppressing recombination, or the spread of epigenetic marks, as the neutral model based on mere nucleotide divergence does not seem to hold in P. anserina.

More information: https://doi.org/10.1093/g3journal/jkaf015

Contact: Pierre GROGNET pierre.grognet@universite-paris-saclay.fr

T-DNAs are mobile elements transferred from pathogenic Agrobacterium to plants that reprogram host cells into hairy roots or tumors, and which are used as disarmed forms to deliver transgenes in plants. Here we review the mechanisms that silence the expression of T-DNAs in transgenic plants as well as during pathogenesis.

Mobile elements known as T-DNAs are transferred from pathogenic Agrobacterium to plants and reprogram the host cell to form hairy roots or tumors. Disarmed nononcogenic T-DNAs are extensively used to deliver transgenes in plant genetic engineering. Such T-DNAs were the first known targets of RNA silencing mechanisms, which detect foreign RNA in plant cells and produce small RNAs that induce transcript degradation. These T-DNAs can also be transcriptionally silenced by the deposition of epigenetic marks such as DNA methylation and the dimethylation of lysine 9 (H3K9me2) in plants. Here, we review the targeting and the roles of RNA silencing and DNA methylation on T-DNAs in transgenic plants as well as during pathogenesis. In addition, we discuss the crosstalk between T-DNAs and genome-wide changes in DNA methylation during pathogenesis. We also cover recently discovered regulatory phenomena, such as T-DNA suppression and RNA silencing-independent and epigenetic-independent mechanisms that can silence T-DNAs. Finally, we discuss the implications of findings on T-DNA silencing for the improvement of plant genetic engineering.

More information: https://academic-oup-com.insb.bib.cnrs.fr/plphys/advance-article/doi/10.1093/plphys/kiae583/7876130

Contact: Angélique DELERIS angelique.deleris@i2bc.paris-saclay.fr