I2BC Paris-Saclay

DciA secures bidirectional replication initiation in Vibrio cholerae.

Replication is initiated bidirectionally in the three domains of life by the assembly of two replication forks at an origin of replication. This is made possible by the recruitment of two replicative helicases to a nucleoprotein platform built at the origin of replication with the initiator protein. The reason why replication is initiated bidirectionally has never been experimentally addressed due to the lack of a suitable biological system. Using genetic and genomic approaches, we show that upon depletion of DciA, replication is no longer initiated bidirectionally at the origin of replication of Vibrio cholerae chromosome 1. We show that following unidirectional replication on the left replichore, nascent DNA strands at ori1 anneal to each other to form a double-stranded DNA end. While this DNA end can be efficiently resected in recB+ cells, only a few cells use it to trigger replication on the right replichore. In most DciA-depleted cells, chromosome 1 is degraded leading to cell death. Our results suggest that DciA is essential to ensuring bidirectional initiation of replication in bacteria, preventing a cascade of deleterious events following unidirectional replication initiation.

More information: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae795/7759985

Contact: Amelie BESOMBES amelie.besombes@i2bc.paris-saclay.fr

How enteric bacteria handle a cold snap

Bacteria that inhabit warm-blooded hosts, particularly enteric pathogens and commensals, often spend prolonged periods outside their hosts in cooler environments. The transition from a warm to a cold external environment typically occurs abruptly when bacteria are released from the host. Understanding how these microorganisms rapidly adapt and thrive at low temperatures is crucial for defining their persistence on contaminated surfaces and their spread to humans and animals.
At the molecular level, the primary effect of cold shock on bacterial physiology is the inhibition of protein synthesis, largely due to increased RNA structuring. Bacteria respond by synthesizing a set of RNA chaperone proteins that either unfold RNA secondary structures or degrade misfolded, untranslatable RNA. The synthesis of these “cold-shock response” (CSR) proteins is driven by cold-induced secondary structures in the 5’ untranslated regions of their mRNAs, which expose ribosome binding sites and facilitate translation initiation. As CSR proteins accumulate, their RNA unfolding activity on their own mRNAs acts as a negative feedback mechanism to reduce synthesis once bacteria acclimate to low temperatures.
In a study published in Molecular Cell, researchers from the I2BC, in collaboration with a group from the CBM, CNRS, Orleans, demonstrated that the very RNA structures that activate CSP mRNA translation act earlier to prevent premature transcription termination by sequestering the binding sites for the termination factor Rho. Remarkably, these conditional terminators function as dual-input, antagonistic riboswitches that regulate Rho access to mRNA based on temperature and CSR protein concentration. Together with established post-transcriptional mechanisms, this allows tight and timely control of CSR gene expression: an initial burst during cold shock followed by attenuation during acclimation. This work establishes a novel paradigm for how RNA thermosensors modulate gene expression.

more information: https://www.sciencedirect.com/science/article/pii/S1097276524006324

Contact: nara.figueroa@i2bc.paris-saclay.fr lionello.bossi@i2bc.paris-saclay.fr

TLN468 promotes PTC readthrough by preferentially incorporating specific tRNAs based on the mutation.

Nonsense mutations account for 12 % of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin.
We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs of CFTR during readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the pro- portions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modu- lators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC sup- pression in combination with CFTR modulators in preclinical assays.

More information: https://www.cysticfibrosisjournal.com/article/S1569-1993(24)00802-6/fulltext

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

Phanie is a phi-29 like phage that protects its genome inside non-infectious podovirus-like particles, requiring acquisition of the tail from a myovirus helper for production of infectious chimeras.

Viruses of bacteria (bacteriophages or phages) display a remarkable genomic diversity reflecting the complex interaction they have built with their host during evolution. In addition to fully infectious viral particles, different types of genetic elements were described to require a helper phage for production of infectious virions. The genome of these satellite parasite sequences may share sequences with phages or be more closely related to non-viral chromosome islands. We describe a new mode of satellite phage dependence on a helper phage. Phanie, like the genetically related Bacillus subtilis phage phi29, replicates its linear dsDNA by a protein primed-mechanism and protects it inside podovirus-like particles. However, these particles are defective, requiring acquisition of the tail from a myovirus helper for production of infectious virions. Formation of chimeras between a phi29-like podovirus and a helper contractile tail reveals an unexpected association between very different bacterial viruses.

More information: https://journals-asm-org.insb.bib.cnrs.fr/doi/10.1128/jvi.00667-24

Contact: Christine Pourcel christine.pourcel@i2bc.paris-saclay.fr

In this work, we reviewed the latest Hi-C findings and discuss the principles of bacterial chromosome folding that can be inferred from them.

The use of Hi-C not only revealed the diversity of 3D-genome architectures in multiple bacterial species across the phylogenetic tree, but also the different scales of genome organization and the mechanisms of action of key structural factors and processes. Here, we revisited the work performed on these bacteria and discussed the rules of genome folding that can be deduced from it.

more information: https://onlinelibrary.wiley.com/doi/10.1111/mmi.15290

contact: Virginia LIOY <virginia.lioy@i2bc.paris-saclay.fr>

In this literature review in Nature Structural and Molecular Biology, scientists from the Institute Jacques Monod and the I2BC discuss how the methylation of DNA changes the folding of our chromosomes and how this can cause defects and disease.

DNA methylation is used as an epigenetic mark on human chromosomes to regulate the transcriptional activity of genes and parasitic transposable elements. Within the nucleus of human cells, chromosomes are non-randomly organized, which strongly influences transcriptional activity as well. DNA methylation and 3D chromosome organization are strongly reorganized during the earliest stages of embryonic development and in diseases like cancer. In this literature review, published in Nature Structural and Molecular Biology, scientists from the Institute Jacques Monod and the I2BC discuss the links between the two levels of chromosome organization. The authors particularly focus on the CTCF insulator protein, whose binding to the DNA directly translates 3D chromosome organization to transcriptional activity. CTCF binding to the DNA has been reported as DNA methylation sensitive in certain contexts, which for certain genes explains the link between transcriptional activity, 3D chromosome organization and DNA methylation. Yet, changes in CTCF binding near other genes appears less obviously coupled to this epigenetic mark, indicating that other mechanisms must play a role as well.

more information: https://www.nature.com/articles/s41594-024-01241-6

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

Positive DNA supercoiling generated ahead of RNA polymerase during transcription elongation dislodges nucleoid-structuring protein H-NS from the DNA.

Bacterial chromosomal DNA is condensed more than 1000 times inside the cell. This condensation results from a slight underwinding of the double helix, leading to the formation of loops of negatively supercoiled DNA (plectonemes) and from interactions with structural proteins that help compact these loops. However, these chromatin-associated proteins obstruct transcription and need to be transiently removed to allow gene expression. This is the case for H-NS, an abundant protein that blocks the expression of numerous genes. In Gram-negative pathogenic bacteria such as Salmonella, H-NS represses the expression of the majority of virulence genes. Displacement of H-NS becomes necessary during the infection process, which relies on the function of virulence gene products.
In a study published in the journal Nature Communications, researchers from the Genome Biology department of the Institute for Integrative Biology of the Cell (I2BC) present evidence that binding of H-NS to DNA is destabilized, from a distance, by the positive supercoils forming ahead of approaching RNA polymerase. It is known that the process of transcription induces DNA supercoiling by forcing the rotation of the DNA axis during elongation. To explain the destabilization of H-NS:DNA complexes by positive supercoiling, the researchers propose a model in which H-NS oligomers play a scaffolding role in negatively supercoiled DNA by bridging opposite arms of the plectonemic structure. Accumulation of positive supercoils and concomitant DNA axis rotation ahead of the approaching RNA polymerase cause the H-NS-bound, negatively supercoiled plectoneme to unroll, leading to the collapse of the scaffold and allowing RNA polymerase to continue on its path. 

More information: https://www.nature.com/articles/s41467-024-47114-w

Contact: Lionelo Bossi lionello.bossi@i2bc.paris-saclay.fr

The MukBEF condensin of E. coli loads at the replication fork and is unloaded at the Ter region by MatP.

Structural maintenance of chromosomes (SMC) complexes share conserved structures and serve a common role in maintaining chromosome architecture. In the bacterium Escherichia coli, the SMC complex MukBEF is necessary for rapid growth and the accurate segregation and positioning of the chromosome, although the specific molecular mechanisms involved are still unknown. Here, we used a number of in vivo assays to reveal how MukBEF controls chromosome conformation and how the MatP/matS system prevents MukBEF activity. Our results indicate that the loading of MukBEF occurs preferentially on newly replicated DNA, at multiple loci on the chromosome where it can promote long-range contacts in cis even though MukBEF can promote long-range contacts in the absence of replication. Using Hi-C and ChIP-seq analyses in strains with rearranged chromosomes, the prevention of MukBEF activity increases with the number of matS sites and this effect likely results from the unloading of MukBEF by MatP. Altogether, our results reveal how MukBEF operates to control chromosome folding and segregation in E. coli.

More information: https://elifesciences.org/articles/91185

Contact: Stéphane DUIGOU <stephane.duigou@i2bc.paris-saclay.fr>

Perturbing the Paramecium transcriptome during somatic development reveals the existence of internuclear feed-forward and feedback transcriptional regulatory loops in a multinucleate unicellular eukaryote.

The single-celled ciliate Paramecium tetraurelia harbors multiple nuclei within its cytoplasm: two germline micronuclei (MIC) dedicated to sexual reproduction and a somatic macronucleus (MAC) responsible for gene expression. During the sexual cycle, the parental MAC undergoes progressive degradation while, in the same cell, new MACs develop from copies of the zygotic MIC. Throughout this process, gene expression primarily occurs in the parental MAC, and clusters of developmentally regulated genes are successively switched on and off. Concomitantly, the genome of the new MACs is extensively rearranged and cleansed of its transposons and other DNA repeats, to become competent for gene expression.

New MAC development has long been known to be controled by the parental MAC, which expresses key genes involved in programmed genome rearrangement (PGR). In this study, RNA deep sequencing and bioinformatic analysis of differential gene expression reveal a reciprocal relationship between the two generations of MACs: the formation of the new MACs is essential for the proper induction of a subset of developmental genes. Later in the sexual cycle, if PGR is hindered in the new MACs, a group of genes partially overlapping the former subset is upregulated, and no longer switched off. Thus, the progression of new MAC development regulates the gene expression program in the parental MAC at different stages. The set of co-expressed genes identified during the course of this work establishes a list of potential novel actors, whose roles in PGR will be explored in future studies.

More information: https://doi.org/10.1093/nar/gkad1006

Contact: Olivier Arnaiz – Mireille Bétermier <olivier.arnaiz@i2bc.paris-saclay.fr> <mireille.betermier@i2bc.paris-saclay.fr>

Clusters of binding sites for the CTCF protein create boundaries between functional domains in the mouse and human genomes. Scientists at the I2BC have determined the characteristics of these clusters and how individual sites contribute to domain separation.

Topologically Associating Domains (TADs) regionalize the human and mouse genome into domains that are essential for processes like gene regulation and DNA repair. Most boundaries between TADs bind the CTCF insulator protein, which is responsible for the blocking of interactions between neighboring TADs. CTCF is thereby directly responsible for improved functional precision and reduced regulatory interference between domains in the genome. Although a clustering of CTCF binding sites had previously been observed at TAD boundaries, its structural impact remained to be determined.
Scientists in the Chromatin Dynamics group at the I2BC, in collaboration with groups at the Ecole Normale Supérieure (Paris) and the University of Pennsylvania (USA), found that three features of CTCF binding are enriched at TAD boundaries, including the presence of closely-spaced copies of its DNA binding motifs, a reduced distance between clusters of motifs and an enrichment of clusters with improved binding affinity. Using Nano-C technology, a new approach to measure the blocking of DNA interactions, they subsequently determined the blocking capacity of individual sites of CTCF binding. These studies reveal that these sites individually contribute to the blocking of interactions between domains, but in an incomplete manner. Grouping of multiple sites of CTCF binding in the genome thus creates a stepwise insulation between neighboring TADs, thereby improving the focus of genomic functions.

More information: https://doi.org/10.1038/s41467-023-41265-y

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

Combined experimental and in-sillico approaches show that the Rif1 protein restricts the activation of replication origins of chromatin domains and the recruitment of initiation factors during the first embryonic divisions.

In multicellular eukaryotic organisms, genomic DNA replicates in a time-controlled manner by ordering early, intermediate, or late replication regions according to a spatio-temporal replication program. How this program is orchestrated is poorly understood, but its dysregulation leads to genomic instability often observed in cancer. The Rif1 protein is a key regulator of this program in eukaryotes; however, its role during the first embryonic cell cycles, when DNA replication is very rapid and replication factors are abundant, remained poorly characterized. Researchers from I2BC, NeuroPSI, ENS Paris, and CalTech (USA) have clarified these mechanisms using the high-performance in vitro system of Xenopus egg extracts by combining the analysis of DNA fibers by molecular combing with an in-sillico model. This study, published in Communications Biology, reveals that in the absence of Rif1, the temporal program of replication is greatly accelerated at the level of groups of origins. This acceleration is accompanied by increased chromatin recruitment of an S phase kinase (Cdc7/Drf1) and several other key factors implicated in the replication initiation (Treslin/MTBP, RecQL4). The model proposed in this study is that Rif1 simultaneously restricts access to DNA or the activity of several factors to fine-tune the exceptionally rapid DNA synthesis observed during embryonic development. A better understanding of the role of Rif1 during these stages opens a way to elucidating the molecular mechanisms involved in certain diseases resulting from Rif1 mutations or variants in humans.
Read on to find out more in Nature Portfolio: https://cellmolbiocommunity.springernature.com/posts/how-rif1-bridles-rapid-embryonic-dna-synthesis

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

DENSE with your favorite genome and uncover its de novo genes! Try our fully automated tool for DE Novo gene SEarch and discover useful metrics to help design your search!

The recent discovery of de novo emerged genes, which originate from previously noncoding regions of DNA, challenges traditional views of species evolution. Indeed, the hypothesis of neutrally evolving sequences giving rise to functional proteins is highly unlikely. However, the accumulation of sequencing data revealed that they are widespread, being detected in various eukaryotic species and numerous, with several dozens of examples reported for different organisms. This conundrum has sparked numerous studies to quantify and characterize these genes, aiming to understand their functional roles and contributions to genome evolution. Yet, no fully automated pipeline for their identification is available. Therefore, we introduce DENSE (DE Novo emerged gene SEarch), an automated Nextflow pipeline based on two distinct steps: detection of taxonomically restricted genes (TRGs) through phylostratigraphy, and filtering of TRGs for de novo emerged genes via genome comparisons and synteny search. DENSE is available as a user-friendly command-line tool, while the second step is accessible through a web server upon providing a list of TRGs. Highly flexible, DENSE provides various strategy and parameter combinations, enabling users to adapt to specific configurations or define their own strategy through a rational framework, facilitating protocol communication, and study interoperability. We apply DENSE to seven model organisms, exploring the impact of its strategies and parameters on de novo gene predictions. This thorough analysis across species with different evolutionary rates reveals useful metrics for users to define input datasets, identify favorable/unfavorable conditions for de novo gene detection, and control potential biases in genome annotations. Additionally, predictions made for the seven model organisms are compiled into a requestable database, which we hope will serve as a reference for de novo emerged gene lists generated with specific criteria combinations.

More information: https://academic.oup.com/gbe/article/16/8/evae159/7745841

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

Unveiling a new property of bacteriophage-host interaction in the context of multicellular aggregate dynamics – A multidisciplinary study involving three departments from I2BC (Genomes, Microbiology, and Virology) and a team from MICALIS.

Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle, and play a key role in soil ecology. Little is known about the impact of Streptomyces-phage on bacterial physiology. In this study, we investigated the conditions governing the expression and production of ‘Samy’, a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. Altogether, this study unveiled a new property of a bacteriophage infection in the context of multicellular aggregate dynamics.

More information: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002725

Contact:  Stéphanie BURY-MONE stephanie.bury-mone@i2bc.paris-saclay.fr

Researchers from the I2BC, the CNRGH (CEA, National Center of Human Genomics Research), and the University of Edinburgh have revealed how the BAF chromatin remodeler changes the structure and accessibility of genetic material by producing subnucleosomal particles. These findings are published in Nature Structural and Molecular Biology.

Mutations in genes encoding subunits of the BAF complex (BRG1/BRM-associated factors, also known as the SWI/SNF complex) are associated with 20% of human cancers, making this complex the second most frequently mutated factor after the p53 tumor suppressor.
The human genome exists in cells in the form of chromatin, composed of nucleosomes that condense and protect the genetic material. The nucleosomes represent a physical barrier for transcription factors and molecular machinery that regulate gene expression. The BAF complex is known for controlling chromatin opening at gene transcription regulatory elements. Until now, it was believed that the role of the BAF complex was to dissociate the nucleosomes to allow the transcription factors to access DNA.
Using a method that allows them to differentiate histone-free DNA fragments from nucleosomes and histone-containing particles smaller than nucleosomes (subnucleosomes), researchers coordinated by Matthieu Gérard (I2BC) revealed that the BAF complex facilitates the recruitment of the master transcription factor OCT4 using two distinct strategies: i) by generating the well-known histone-free DNA regions, which OCT4 binds if its target DNA motif is present; and ii) by producing a new class of subnucleosomal particles containing 50 to 80 base pairs associated with histones.
They show that the subnucleosomes act as a recruitment platform for OCT4 independently of the presence of its DNA motif. They identify in this publication a molecular mechanism in which the interaction between OCT4 and the subnucleosomes leads to a spectacular expansion of the OCT4 genomic binding interval. This mechanism aims to project OCT4 activity in chromatin opening within a genomic interval up to one order of magnitude larger than the interval bound by OCT4 on histone-free DNA.
This study suggests two main determinants for recruiting transcription factors onto the mammalian genome: the genetic determinant, the transcription factor motif within histone-free DNA, and an epigenetic determinant, which corresponds to the subnucleosomes produced by the BAF complex.

More information: https://www.nature.com/articles/s41594-024-01344-0

Contact: Matthieu GERARD matthieu.gerard@i2bc.paris-saclay.fr

The Dlk1-Meg3-Dio3 domain is imprinted. Scientists at the IGMM and the I2BC have determined that Meg3 long non-coding RNA, as well as DNA methylation levels at an essential CTCF binding site in the domain, control Dlk1 imprinting in cis.

The imprinted Dlk1-Dio3 domain comprises the Dlk1 and Rtl1 developmental genes that are solely expressed from the paternal chromosome, and a maternally-expressed polycistron that is further processed into the Meg3 long non-coding RNA (lncRNA) and many other small non-coding RNAs.

In collaborative work between scientists at the IGMM (R. Feil’s group; Montpellier) and at the I2BC (D. Noordermeer’s group; Gif-sur-Yvette), researchers studied the precise role of Meg3 lncRNA and of its promoter for the control of Dlk1 and Rtl1 imprinted gene expression. Using mutant cells with either premature termination of transcription or deletion of part of the polycistron, they found that Meg3 lncRNA, but not other non-coding RNAs produced by the polycistron, controls Dlk1 imprinting in cis.

The maternal expression of this polycistron is driven by the Meg3 differentially methylated region (Meg3-DMR) which is unmethylated on the maternal allele and acts there as an active promoter. Besides, the Meg3-DMR includes a known binding site for the architectural CTCF protein, that binds to the unmethylated maternal allele only. In this study, the researcher showed that the maternal Dlk1-Dio3 locus is organized into sub-Topologically Associating domains (sub-TADs) that are hinged by the allelic binding of CTCF to the maternal Meg3-DMR. They further found that the methylation levels at the Meg3-DMR are instructive for CTCF binding and thereby dictate distinctive sub-TAD organization at the two parental alleles which, in turns, facilitates Dlk1 repression on the maternal allele.

Altogether, this collaborative work revealed that, the maternally-expressed Meg3 lncRNA controls Dlk1 silencing in cis, and that the low methylation levels at the maternal Meg3-DMR allows for specific sub-TADs structuration that concurrently contributes to Dlk1 silencing.

More information: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae247/7645245?searchresult=1

Contact: Benoit Moindrot benoit.moindrot@i2bc.paris-saclay.fr 

Chloé @Chl0e_Girard and Daan @DaanNoordermeer were invited to an interdisciplinary workshop organized by the Bettencourt-Schueller Foundation @Fondation_BS about creativity as motor for scientific research.

A 3-days seminar was organized by the Bettencourt-Schueller Foundation at the Domaine de Chaumont-sur-Loire for former laureates (Prix Jeune Chercheur, Prix Impulsience, Prix Coups d’Elan pour la Recherche Française). This interdisciplinary seminar centered around creativity combined Arts & Science, the two main components of the foundation's patronage. The I2BC scientists participated in thematic workshops around Music, Mathematics, Visual Arts and Biology, presented by world-reknown artists and scientists. Daan Nordermeer was a recipient of the "Coup d'élan pour la recherche française”, while Chloé Girard received the "Prix jeune Chercheur", both in 2015.

We show that the regulation and compartmentalisation of nucleosomal organisation require the concomitant actions of local and global processes that are maintained actively by energy consuming factors.

In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as tran- scription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic proper- ties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler—which is responsible for NDR maintenance—is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which inter- fere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome orga- nisation, whilst Chd1 plays a key role for maintaining local arrangement.

More information: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011799

Contact: Arach GOLDAR <arach.goldar@i2bc.paris-saclay.fr>

It has become easier to build 3D models of the entire genome based on Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration.

The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in Saccharomyces cerevisiae, the backbones of the cohesin anchor regions, which were aligned all along the chromosomes, (ii) in Schizosaccharomyces pombe, the oscillations of the coiling of chromosome arms throughout the cell cycle and (iii) in Neurospora crassa, the massive relocalization of histone marks in mutants of heterochromatin regulators. 3D modeling of the chromosomes brings new opportunities for visual integration of omics data. This holistic perspective supports intuition and lays the foundation for building new concepts.

More information: https://academic.oup.com/nargab/article/5/4/lqad104/7458894

Contact: Gaëlle LELANDAIS <gaelle.lelandais@i2bc.paris-saclay.fr>

Meet Alicia Nevers, an assistant professor of Paris-Saclay University, that just joined the Genome Biology Department of the I2BC.

Alicia began her undergraduate studies with a DUT in Biological Engineering, which she obtained in 2011. She then went on to complete a Bachelor's degree in Life Sciences, followed by a Master's degree in Molecular and Cellular Biology, with a specialization in RNA Molecular Biology. From 2013 to 2017, she did her thesis with the Université Paris Sorbonne and in Alain Jacquier's laboratory at the Institut Pasteur. Under the supervision of Alain Jacquier and Gwenaël Badis-Bréard she studied, in the budding yeast Saccharomyces cerevisiae, the mechanisms of control of gene expression by transcriptional interference and the functionality of pervasive antisense transcription. Alicia then joined Mathieu Rougemaille's laboratory at I2BC as a research engineer between 2018 and 2020. She contributed to the discovery and characterization of a novel non-coding RNA involved in the control of meiosis in the fissiparous yeast Schizosaccharomyces pombe. After that, Alicia was hosted in Micalis Unit of Inrae as a post-doctoral researcher. Here, under the supervision of Didier Lereclus, Michel Gohar and Vincent Sanchis-Borja, she studied the role megaplasmids in new pathogens emergence. More particularly she studied pCER270 megaplasmid, representative of emetic strains of Bacillus cereus group. She particularly analyzed in natural and artificial hosts, the consequences of pCER270 presence for gene expression and biofilm formation ability. Now that she joined Frédéric Boccard’s laboratory as a senior lecturer, she’ll work under the supervision of Vicky Lioy and Stéphany Bury-Moné to describe a link between gene expression, chromosome conformation and bacterial lifestyle, in particular biofilm formation, in the pathogen Pseudomonas aeruginosa.

Review in Trends in Genetics: Towards an integrated view of Streptomyces chromosome dynamics in space and time

Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. Remarkably, these bacteria possess a large linear chromosome that is genetically compartmentalized: core genes are grouped in the central part, while the ends are populated by poorly conserved genes including antibiotic biosynthetic gene clusters. The genome is highly unstable and exhibits distinct evolutionary rates along the chromosome. Recent chromosome conformation capture (3C) and comparative genomics studies have shed new light on the interplay between genome dynamics in space and time. Here, we review insights that illustrate how the balance between chance (random genome variations) and necessity (structural and functional constraints) may have led to the emergence of spatial structuring of the Streptomyces chromosome.

More information: https://www.cell.com/trends/genetics/fulltext/S0168-9525(23)00166-X

Contact: Stéphanie BURY-MONE <stephanie.bury-mone@i2bc.paris-saclay.fr>

Our chromosomes are divided into strucrural domains that focus biological activity. In this literature review, researchers from the I2BC summarize recent insights into the dynamic nature of this process, and how this nonetheless can create stable regulation.

Mammalian chromosomes are organized at different length scales within the cell nucleus. Topologically Associating Domains (TADs) are structural units of 3D genome organization that compartmentalize chromosomes into separated domains. Within these domains, biological functions are focused, thereby restricting the “spread” of gene regulation, DNA replication, recombination and repair. In this review, published in Current Opinion in Structural Biology, scientists from the Chromatin Dynamics team at the I2BC discuss recent insights into the structure and function of TADs. Whereas TADs were initially interpreted as insulated domains, recent studies are revealing that these domains should be interpreted as dynamic collections of actively extruding loops. This process of loop extrusion is subsequently blocked at dedicated TAD boundaries, thereby promoting intra-domain interactions over their surroundings. The authors discuss how mammalian TAD structure can emerge from this dynamic process and they discuss recent evidence that boundaries between TADs can have regulatory functions.

More information: https://www.sciencedirect.com/science/article/abs/pii/S0959440X23000969

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