I2BC Paris-Saclay

The fission yeast Ccr4-Not complex promotes propagation of the repressive H3K9me3 histone mark to mediate heterochromatic gene silencing.

Eukaryotic genomes are partitioned into relaxed, gene-rich regions and condensed, gene-poor domains called heterochromatin. The maintenance of heterochromatin is crucial for proper genome expression and integrity, and requires multiple factors regulating histone modifications and/or the levels of RNA molecules produced from these regions. Such effectors not only promote heterochromatin assembly but also ensure its propagation from specific nucleation sites to defined domain boundaries. However, while the mechanisms involved in initiation of heterochromatin formation have been well documented, the molecular and biochemical properties underlying its spreading remain largely elusive. By combining genetic and single-cell approaches, we report here that the fission yeast Ccr4-Not complex, a multisubunit complex conserved throughout eukaryotes, is essential for efficient heterochromatin spreading to repress expression of nucleation-distal RNAs. The two catalytic activities of the complex, RNA deadenylation and protein ubiquitinylation, are each critical, thereby defining a dual enzymatic requirement in the process.

More information: https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad108/7190671?login=false

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

Physical interaction and functional interplay between essential co-regulators in transcription and chromatin organization, Mediator and RSC chromatin remodeler, contributes to nucleosome-depleted region formation at promoters and +1 nucleosome positioning.

Eukaryotic DNA is compactly structured through chromatin organization which governs and influences all DNA transactions. Regulation of transcription is a key phenomenon of gene expression whose alterations lead to severe human pathologies. Multisubunit coregulator complexes can act on chromatin structure as chromatin modifiers or remodelers, or stimulate the assembly of the transcriptional machinery. Mediator is an essential and conserved coactivator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. The team of J. Soutourina (Genome biology/I2BC and Institute Joliot, CEA/CNRS/Paris-Saclay) provides evidence in the budding yeast that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. The role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy and transcription was determined on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and stability of +1 nucleosome associated with transcription-start site. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.

More information: doi.org/10.1016/j.celrep.2023.112465 

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

Understanding how to properly analyze your interspecies gene expression datasets.

Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available methods in various settings. However, synthetic dataset simulation tools are still missing in the interspecies gene expression context. In this work, we develop and implement a new simulation framework. This tool builds on both the RNA-Seq and the phylogenetic comparative methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the usefulness of this new framework through a targeted simulation study, that reproduces the features of a recently published dataset, containing gene expression data in adult eye tissue across blind and sighted freshwater crayfish species. Using our simulated datasets, we perform a fair comparison of several approaches used for differential expression analysis. This benchmark reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for interspecies differential expression analysis, and allows for a reanalysis of the crayfish dataset. The tool has been integrated in the R package compcodeR, freely available on Bioconductor

More information: https://academic.oup.com/mbe/article/40/1/msac269/6889356

Contact: Melina Gallopin <melina.gallopin@i2bc.paris-saclay.fr>

Thanks to multiple RNA-seq data available on public databases, we were able to improve the genome annotation on Podospora anserina and predict important regulatory features such as UTRs, alternative splicing and new transcription units.

Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5’UTR and 3’UTR were defined for 7554, among which, 3328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3’splice sites and 1732 novel transcriptionally active regions (nTARs) in unannotated regions were identified. Our study provides a comprehensive genome-wide functional annotation of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of noncoding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.

More information: https://rdcu.be/c2C2M

Contact: Pierre Grognet <pierre.grognet@i2bc.paris-saclay.fr>

Ribosomal RNA operon-based evolutionary history in Streptomyces: rrn operons define a functional compartment prone to transcription and are close to pericentric inversions. Towards the existence of functional compartments in bacteria?

Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genetic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons are structural boundaries of a central functional compartment prone to transcription in Streptomyces.

More information: here

Contact: Stephanie Bury-Mone <stephanie.bury-mone@i2bc.paris-saclay.fr>

Post-transcriptional control by a small regulatory RNA allows the opportunistic pathogen Staphylococcus aureus to spare iron under iron-starved conditions and increase its pathogenicity.

In response to microbial aggression, host organisms sequester essential nutrients including iron to limit the growth of pathogens. This defense mechanism is called nutritional immunity. Staphylococcus aureus, a pathogen that causes many diseases worldwide, has developed strategies to cope with many adverse growth conditions including surviving within the host. Using a competition assay that we developed, we identified IsrR as a unique small regulatory RNA (sRNA) required for optimal growth in iron-depleted environments. Unlike most staphylococcal sRNAs, IsrR is conserved throughout the genus Staphylococci. Its expression is induced under iron deficiency conditions and its function is to downregulate non-essential enzymes containing iron. Among them, we show that IsrR down-regulates enzymes catalyzing the anaerobic nitrate respiration by blocking the translation of their corresponding mRNA. The structures of IsrR alone and in interaction with its targets were determined in collaboration with Bruno Sargueil's team from Université Paris Cité. The absence of IsrR which leads to a growth defect in iron-starved media is also responsible for reduced virulence (in collaboration with Brice Felden's team, Université Rennes 1), presumably because IsrR is required for the resistance of S. aureus to nutritional immunity.

More information here

Contact: Philippe Bouloc <philippe.bouloc@i2bc.paris-saclay.fr>

An unusual asymmetric domain-swapped dimer.

Deinococcus radiodurans is a spherical bacterium well known for its exceptional resistance to DNA damaging agents. One of the DNA damage response genes specifically encoded by this bacterium, named DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro, we have previously shown that DdrC compacts circular DNA, circularizes linear DNA, anneals complementary ss-DNA and protects DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at 2.5 Å resolution and further characterized its DNA binding and compaction properties. In particular, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and compaction level of circular DNA. These results suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damage conditions.

More information here

Contact: Fabrice Confalonieri <fabrice.confalonieri@i2bc.paris-saclay.fr>

Stochastic transcriptional activity primes self-sustaining positive feedback loop: a novel mechanism for the production of inheritable cell-to-cell differences in a population of genetically identical bacterial siblings.

In growing Salmonella bacteria, expression of a major pathogenicity island — the 44 Kb Salmonella Pathogenicity Island 1 (SPI-1) — shows a typical bimodal distribution characterized by the continuous generation of cells that either express or do not express SPI-1 genes. Like other genomic islands acquired through horizontal transfer, SPI-1 is bound by H-NS, a nucleoid-associated protein that oligomerizes along the DNA starting from high-affinity nucleation sites. H-NS binding is responsible for gene silencing in the SPI-1OFF subpopulation, while silencing is relieved in SPI-1ON cells. This study, aimed at elucidating the mechanism responsible for the partitioning of the two subpopulations, revealed that the OFF-to-ON switching results from the stochastic activity of a number of spurious antisense promoters in a region at some distance from the gene for SPI-1 master regulator, HilD. Transcription complexes assembled at these spurious promoters can occasionally elongate into the hilD gene transiently dislodging H-NS from the DNA and making the hilD promoter directly accessible to RNA polymerase. Once HilD accumulates, the ability of this protein to activate its own gene transcription (by outcompeting H-NS for binding to the hilD promoter) triggers a positive feedback loop that leads to a further increase in HilD levels and results in the transcriptional activation of the entire SPI-1. The self-perpetuating nature of the loop allows for the SPI-1ON phenotype to propagate for a number cell divisions. These data suggest that stochastic events associated with spurious transcription play a major role in the generation of inheritable cell-to cell differences in bacterial populations. 

More information here

Contact: Nara Figueroa et Lionello Bossi <nara.figueroa@i2bc.paris-saclay.fr> <lionello.bossi@i2bc.paris-saclay.fr>

The CTCF protein shapes our chromosomes to make sure that genes are correctly activated in our cells. In this review, Segueni and Noordermeer summarize how the functions of this protein can be perturbed in numerous ways in cancer cells.

Human cells need to precisely regulate the activity of their genes, making sure that in our bodies, each gene is active at the right place, at the right time and in the right amount. Incorrect gene activity is a leading cause of diseases, including cancers. The three-dimensional folding of human chromosomes is an important contributor to gene activity. A key factor in this process is a DNA-binding protein called CTCF, which acts as a “jack-of-all-trades” to organize chromosomes into different levels of folding. All these levels differently contribute to gene activity, thereby maintaining the essential balance for correct cell functions. Unsurprisingly, numerous perturbations of CTCF functions have been implied in different types of cancers. In this literature review, Segueni and Noordermeer have summarized recent insights into how diverse CTCF dysfunctions lead to oncogenesis. Incorrect binding of CTCF to chromosomes is the most common cause of perturbed gene regulation. While such changes in binding can be caused by changes to the CTCF protein itself, they are mostly due to changes in the DNA sequence or DNA methylation at the CTCF binding sites in the chromosomes. These differences in binding can lead to “enhancer hijacking” where disrupted chromosome folding permits unwanted contacts between oncogenes and activating elements in the genome. A number of non-canonical functions of CTCF in the emergence of cancers is discussed as well. To provide guidance for the analysis of CTCF perturbations, a computational strategy for genomics data is introduced to link changes in CTCF binding with reorganized chromosome folding in cancer cells. Based on its diversity of functions, a better understanding of CTCF perturbations can ultimately open up new opportunities for the development of treatments and therapies in different cancers.

More information: https://doi.org/10.1016/j.csbj.2022.05.044

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

A new, robust continuous high-trough put test to screen and characterize new acetyltransferases.

Protein N-acetyltransferases (NATs) belong to the general control non-repressible 5 (Gcn5)-related N-acetyltransferases (GNATs) superfamily. GNATs catalyze the transfer of acetyl from acetyl-CoA to the reactive amine moiety of a wide range of acceptors. NAT sequences are difficult to distinguish from other members of the GNAT superfamily and there are many uncharacterized GNATs. To facilitate the discovery and characterization of new GNATs, we have developed a new continuous, non-radioactive assay. This assay is virtually independent of the substrate and can be used to get substrate specificity hints. We validated first the assay with the well-characterized Schizosaccharomyces pombe NatA (SpNatA). The SpNatA kinetic parameters were determined with various peptides confirming the robustness of the new assay. We reveal that the longer the peptide substrate the more efficient the enzyme. As a proof of concept of the relevance of the new assay, we characterized a NAA90 member from rice (Oryza sativa), OsGNAT2. We took advantage of an in vivo medium-scale characterization of OsGNAT2 specificity to identify and then validate in vitro several specific peptide substrates. With this assay, we reveal long-range synergic effects of basic residues on OsGNAT2 activity. Overall, this new, high-throughput assay allows better understanding of the substrate specificity and activity of any GNAT.

More information: https://pubmed.ncbi.nlm.nih.gov/35273627/

Contact: Carmela Giglione <carmela.giglione@i2bc.paris-saclay.fr>

Uncharted, unannotated RNAs contribute to cancer patient stratification and constitute novel theraputic targets.

Cancer alters our RNAs in many ways, producing a wide diversity of aberrant RNAs of which many are specific to tumor types. Computational RNA sequence analysis in oncology typically focuses on specific RNA families such as mRNAs. Here we undertook to capture at once all RNAs found in lung cancer. To this aim we selected two lung cancer cohorts with 737 RNA sequence sets from lung biopsies, and we applied a technique called k-mer differential analysis, where we identify all RNA fragments that are either over or under-expressed in tumors. We then focused on fragments that were not previously known (uncharted RNAs) and reproducibly observed in both cohorts. Here is what we found:
– Uncharted RNAs come from many different locations (introns, intergenic regions, repeats) and in many forms (spliced, polyadenylated, chimeric etc.)
– A limited set of hypervariable genes such as immunoglobulins contribute a large amount of uncharted RNAs
– Uncharted RNAs from human retroelements define patient subclasses with distinct clinical and genomic features, a well documented phenomenon in cancer
– several uncharted RNAs, including one from a lung bacterium, correlate with the presence of specific immune cells.
– A number of uncharted can be translated and produce tumor-specific antigens that could be targeted by anti-cancer drugs
We hope to convince readers that large amounts of non-reference RNAs of functional significance remain hidden in bulk RNA-seq data.

More information: https://academic.oup.com/narcancer/article/4/1/zcac001/6519484?searchresult=1

Contact: Daniel Gautheret <daniel.gautheret@i2bc.paris-saclay.fr>

Research on conjugation unveiled that recipient chromosome-encoded UvrD helicase plays role in plasmid acquisition, shedding light on important DNA actions in the early stage of transconjugant cell establishment.

Conjugative plasmids are a major dissemination source of resistance to antibiotics in bacterial populations. Even though they encode genes necessary and sufficient for their horizontal transmission, other environmental and genetic factors can alter the efficiency of plasmid transmission. In this study by using Transposon-insertion site sequencing and genetics experiments, we showed that defects in a conserved DNA helicase, UvrD impairs transfer of various conjugative plasmids. This was observed specifically in the recipient cell, not in the donor cell. During conjugation, one strand of plasmid DNA transfers from the donor to the recipient cell. By time-lapse microscopy with sophisticated monitoring tools to detect single-stranded (ss) and double-stranded (ds)DNA, we showed that UvrD plays a role in successful ss to ds conversion of the acquired DNA. An interesting spin is that UvrD homologs are well-known to be multifunctional and many of them are involved in different DNA repair pathways. Our work showed that in addition to its role in maintaining genome integrity, UvrD is also key for the establishment of horizontally acquired DNA that drives genome diversity and evolution.

More information: https://doi.org/10.1093/nar/gkad075

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

A new study has dissected the complex interactions between regulatory layers that fine-tune the activity of a gene which is essential for the correct formation of the embryo.

The formation of the embryo, from humans to flies, requires a precise orchestration of gene activity: genes need to be turned on at the right time, the right place and at the right level. This regulation of activity incorporates different layers, including the activation of regulatory elements through transcription factor binding, the separation between regulatory regions in the genome through insulator protein binding at boundaries, the epigenetic modifications of large stretches of DNA and the higher-order conformation of chromosomes. How these regulatory layers interact among each other, and particularly how they may instruct each other, remains poorly understood. In this study, PhD student Laura Moniot-Perron in the Chromatin Dynamics group of the I2BC, under the supervision of Daan Noordermeer and Sébastien Bloyer, has studied this question for the Abd-B gene, a prototype gene for embryogenesis. The Abd-B gene encodes a transcription factor that specifies segmental identities along the Antero-Posterior (head-to-tail) body axis. At different positions along this body axis, the gene is activated by different regulatory elements that are located increasingly nearby on the chromosome at more posterior positions. Until now, the question how different regulatory layers are involved in the differential activity along the body axis remained largely unknown. Comparison of cells from different positions along the Antero-Posterior axis revealed the importance of the Fab-7 boundary to create different domains of epigenetic modifications and higher-order chromosome conformation. The resulting cell type-specific organizations differentially activate the different promoters of the Abd-B gene, thereby revealing new possibilities to precisely fine-tune the activity of genes involved in embryogenesis.

More information: https://doi.org/10.1016/j.celrep.2022.111967

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

At the crossroads of two different time-scales: how mechanistic constraints on somatic DNA elimination during development have streamlined Paramecium transposon-related sequences in the germline during evolution.

Transposable elements (TEs) have colonized the genomes of all living organisms. Because TE integration events disrupting coding sequences can severely compromise host fitness or survival, they have generally been counter-selected, especially in the germline. With its nuclear dimorphism, the ciliate Paramecium provides a powerful unicellular model to study how eukaryotic genomes cope with TE invasion. Indeed, its germline genome, hosted in the transcriptionally silent micronuclei (MIC), has been invaded by numerous TEs and TE-related sequences, including inside genes. Gene expression takes place in a polyploid somatic macronucleus (MAC) that is destroyed at each sexual cycle, while a new MAC is formed from a copy of the MIC. New MAC development involves extensive DNA amplification, massive TE elimination and the precise excision of thousands of short TE-derived sequences called Internal Eliminated Sequences (IESs). Programmed DNA elimination is mainly guided by non-coding RNAs and repressive chromatin marks.
To gain insight into how Paramecium IESs are targeted for elimination, the “Programmed genome rearrangements” team embarked on a genome-wide study of the developmental timing of DNA elimination, in collaboration with the Cytometry and Sequencing platforms of I2BC. By combining fluorescence-assisted nuclear sorting with high-throughput DNA sequencing, they established the developmental time-course of DNA elimination at unprecedented resolution. They showed that IESs are excised following a sequential order that reflects their evolutionary age. The most ancient elements have evolved in optimizing their excision efficiency, acquiring strong sequence determinants and escaping epigenetic control.

More information: https://genome.cshlp.org/content/early/2022/11/22/gr.277027.122.abstract

Contact: Vinciane Regnier  <vinciane.regnier@i2bc.paris-saclay.fr> & Mireille Bétermier <mireille.betermier@i2bc.paris-saclay.fr>

The Genome Biology department of the I2BC created its own logo!

During the last months, Pierre Grognet launched a contest inviting all the Genome Biology (GB) researchers to create an official logo for the department. Fourteen great creations were submitted for voting, all of them representing the spirit of the department. With a participation of more than 50%, and after a second round of votes to break the tie, the new logo was selected. Thank to all the researchers that participated and congratulations to Stéphanie Bury-Moné, the creative mind behind the new logo. Stéphanie explained to us that she created a logo in the I2BC style, with the GBD colors, represented in the triangle. According to Stéphanie, the logo also represents the science carried out in the department: “in the center, a DNA double helix with a perspective effect seems to open a way to future research or applications; the circle could represent a RNA chain, and the triangle a protein bound to it. These are the multiple facets of our research activities within our department". The new logo will used in the webpage of the GB department and also in all the official documents. You can find the GB logo on the intranet of the I2BC (Documents and administrative tools/Logos)

Personalized medicine: how to repair a defective gene without modifying the genome?

Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).

More information here

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

Apicomplexa N-acetylation independent of AT1.

Acetylation of secreted proteins occurs post-translationally to regulate their function and secretion. This process is believed to take place in the ER and requires acetyl-CoA, a metabolite that is transported into the ER by a membrane acetyl-CoA transporter (AT1). N-acetyltransferases (NATs) transfer acetyl groups from acetyl-CoA to the N-termini of proteins and N-terminal acetylation is known to occur in Apicomplexa parasites, including Toxoplasma gondii, which causes toxoplasmosis and Plasmodium berghei a rodent malaria model. However, the importance of acetyl-CoA and its ER transport has not been assessed in these species. In this study, Carmela Giglione and colleagues (Nyonda et al., 2022) identify homologues of AT1 and NAT8 in these parasites. They report that deletion of AT1 gene impairs erythrocytic proliferation of P. berghei and reduces overall parasite fitness. Additionally, female gametocytogenesis and male gametogenesis, which are required for transmission to the mosquito, are attenuated by AT1 deficiency, despite having no detectable impact on the global levels of N-terminal and lysine acetylation. In T. gondii, AT1deletion causes defective growth in the lytic cycle but invasion of host cells is not impaired. Overall, these findings highlight the importance of AT1 in P. berghei development and malaria transmission. However, the preservation of N-terminal and lysine acetylation in AT1-deficient mutants suggests an uncoupling between AT1 function in development and active acetylation in the secretory pathway and that a bypass alternative route ensures acetyl-CoA import along the secretory pathway in the absence of AT1.”

More information here

Contact: Carmela Giglione  <carmela.giglione@i2bc.paris-saclay.fr>

Using different facets of the versatile Xenopus model system, this study uncovered a new function of the Yap oncogene by showing that it slows the progression of the rapid embryonic S phase in conjunction with the key DNA replication-timing factor Rif1.

In multicellular eukaryotic organisms, the initiation of DNA replication asynchronously occurs at specific sites, replication origins, throughout the S phase of the cell cycle, following a replication-timing program. How this program is regulated is poorly understood, but its deregulation provokes genomic instability and cancer. Using different facets of the Xenopus model system, O. Haccard, N. Narassimprakash, and K. Marheineke, in collaboration with the team of M. Perron (NeuroPSI), have shown that Yap (Yes-associated protein 1), a downstream effector of the Hippo signaling pathway, is required for the control of DNA replication dynamics. They uncovered that Yap is recruited to chromatin at the start of DNA replication and identified Rif1, the primary regulator of the DNA replication-timing program, as a novel Yap binding protein. Moreover, they show that either Yap or Rif1 depletion accelerates DNA replication dynamics by increasing the number of activated replication origins. Thanks to an innovative approach, based on the Trim-Away technique, applied to Xenopus embryos during early cleavage stages devoid of transcription, they found that either Yap or Rif1 depletion triggers an acceleration of cell divisions. This suggests a shorter S phase caused by the alteration of the replication program. Finally, their data show that Rif1 in vivo knockdown leads to defects in the partitioning of early versus late replication foci in retinal stem cells, as M. Perron's team had previously demonstrated for Yap. Altogether, these findings unveil a new, non-transcriptional role for Yap in regulating replication dynamics. Yap and Rif1, therefore, seem to function as brakes to control the DNA replication program in early embryos and post-embryonic stem cells.

More information here

Contact: Kathrin Marheineke <kathrin.marheineke@i2bc.paris-saclay.fr>

The polar anchoring HubP involved in partition system of Vibrio cholerae chromosome I (ch1) is dispensable for an active positioning of ch1 replication origin but is required for the normal longitudinal organization of ch1.

Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1 (parS2::parS1). Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle.

More information: https://www.mdpi.com/2073-4425/13/5/877

Contact: Christophe Possoz <christophe.possoz@i2bc.paris-saclay.fr>

After two years, the whole Genome Biology Department meet in person to celebrate the VI Genome Biology Day.

Last May 20th the Genome Biology Department met during a whole day to present and discuss the research projects carried out by the researchers of the department. Great short talks and posters covering studies on bioinformatics and genomics; gene expression and regulation; and dynamics and stability of genomes were presented during the day. In addition, two keynote talks were presented by Cynthia Sharma (University of Würzburg, Germany) and Ian Henderson (University of Cambridge, UK). Cynthia’s talk covered novel aspects of gene regulation by non-coding RNAs in Helicobacter pylori and Campilobacter jejeuni. Ian’s presentation focused into how the the Arabidopsis pan-centromere revealed the contribution of transposable elements on centromere evolution. At the end of the day, the winners of the ‘Best Talk Awards’ (James Provan, Barre’s lab & Kevin André, Souturina’s lab) and of the ‘Best Poster Awards’ (Amelie Besombes, Barre’s Lab; Kam Pou Ha, Bouloc’s lab and Estelle Leroy, Rougmaille’s lab) were announced. Altogether, this was a great day in which the GB department could meet and discuss about their favorite research topic: The Biology of Genomes.

Contact: organizing commeette <virginia.lioy@i2bc.paris-saclay.fr>,<yoshiharu.yamaichi@i2bc.paris-saclay.fr> & <angelique.deleris@i2bc.paris-saclay.fr> 

Plesiomonas shigelloides, an atypical Enterobacterales with a Vibrio-related secondary chromosome

Vibrionales and Enterobacterales are two closely related orders that derive from a common ancestor. While Vibrionales are multi-chromosome species, Enterobacterales are known to be mono-chromosome bacteria. What are the features and factors needed to ensure the sustainability of multiple chromosomes in a cell? We addressed this question by searching and identifying an Enterobacterium with multiple chromosomes, Plesiomonas shigelloides, and by carring out a comparative analysis of its genome and proteome with those of the mono-chromosome Enterobacterales and the multi-chromosome Vibrionales.

More information: https://academic.oup.com/gbe/article/14/2/evac011/6515279?login=true

Contact: Jean-Luc FERAT <jean-luc.ferat@i2bc.paris-saclay.fr>