Annuaire
Publications
Les 20 dernières publications
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Topological Constraints and Finite-Size Effects in Quantitative Polymer Models of Chromatin Organization
- Journal : Macromolecules
- 2023
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Transcription induces context-dependent remodeling of chromatin architecture during differentiation.
- Journal : PLoS Biol
- 2023
- Metazoan chromosomes are organized into discrete spatial domains (TADs), believedto contribute to the regulation of transcriptional programs. Despite extensivecorrelation between domain organization and gene activity, a direct mechanisticlink is unclear, with perturbation studies often showing little effect. To followchromatin architecture changes during development, we used Capture Hi-C tointerrogate the domains around key differentially expressed genes during mousethymocyte maturation, uncovering specific remodeling events. Notably, one TADboundary was broadened to accommodate RNA polymerase elongation past the border,and subdomains were formed around some activated genes without changes in CTCFbinding. The ectopic induction of some genes was sufficient to recapitulatedomain formation in embryonic stem cells, providing strong evidence thattranscription can directly remodel chromatin structure. These results suggestthat transcriptional processes drive complex chromosome folding patterns that canbe important in certain genomic contexts.
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Histone removal in sperm protects paternal chromosomes from premature division at fertilization
- Journal : Science
- 2023
- The global replacement of histones with protamines in sperm chromatin is widespread in animals, including insects, but its actual function remains enigmatic. We show that in the Drosophila paternal effect mutant paternal loss ( pal ), sperm chromatin retains germline histones H3 and H4 genome wide without impairing sperm viability. However, after fertilization, pal sperm chromosomes are targeted by the egg chromosomal passenger complex and engage into a catastrophic premature division in synchrony with female meiosis II. We show that pal encodes a rapidly evolving transition protein specifically required for the eviction of (H3-H4) 2 tetramers from spermatid DNA after the removal of H2A-H2B dimers. Our study thus reveals an unsuspected role of histone eviction from insect sperm chromatin: safeguarding the integrity of the male pronucleus during female meiosis. , Editor’s summary Ultracompaction of sperm DNA in many species is often associated with genome-wide replacement of histones with protamines, but the actual role of this radical change in chromatin organization remains largely enigmatic. Looking at a multidecade-old Drosophila mutant, Dubruille et al . found that histones were massively retained in sperm without affecting its ability to fertilize (see the Perspective by Levine). However, at fertilization, male chromosomes were aberrantly recognized by maternal factors that control female meiotic progression, leading to a deleterious premature division and early loss of male chromosomes. This work highlights the role of sperm chromatin in protecting male chromosomes in the egg. —Di Jiang , Histone retention in Drosophila sperm chromatin jeopardizes paternal chromosome integrity during female meiosis.
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RNA Pol II antagonises mitotic chromatin folding and chromosome segregation by condensin
- Journal : BioRIXV (Cell Reports, in revision)
- 2023
- Condensin shapes mitotic chromosomes by folding chromatin into loops but whether it does so by DNA-loop extrusion remains speculative. While loop-extruding cohesin is stalled by transcription, no conclusive evidence has been provided regarding the impact of transcription on condensin despite its conserved enrichment at highly expressed genes. Using degrons of Rpb1 or the torpedo nuclease Dhp1XRN2, we depleted or displaced RNAP2 on chromatin in fission yeast metaphase cells. We show that RNAP2 does not load condensin on DNA but instead retains condensin and hinders its ability to fold mitotic chromatin and to support chromosome segregation, consistent with the stalling of a loop-extruder. Transcription termination by Dhp1 limits such a hindrance. Our results shed a new light on the integrated functioning of condensin and we argue that a tight control of transcription underlies mitotic chromosome assembly by loop-extruding condensin.Competing Interest StatementThe authors have declared no competing interest.
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Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase
- Journal : eLife
- 2023
- The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome-remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
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SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans.
- Journal : Development
- 2023
- The SIN3 transcriptional coregulator influences gene expression through multipleinteractions that include histone deacetylases (HDACs). Haploinsufficiency andmutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and relatedintellectual disability (ID)/autism syndromes, emphasizing its key role indevelopment. However, little is known about the diversity of its interactions andfunctions in developmental processes. Here we show that loss of SIN-3, the singleSIN3 homologue in Caenorhabditis elegans, results in maternal effect sterilityassociated with deregulation of the germline transcriptome, including desilencingof X-linked genes. We identify at least two distinct SIN3 complexes containingspecific HDACs, and show that they differentially contribute to fertility. Singlecell smFISH reveals that in sin-3 mutants, the X chromosome becomes re-expressedprematurely and in a stochastic manner in individual germ cells, suggesting arole for SIN-3 in its silencing. Furthermore, we identify histone residues whoseacetylation increases in the absence of SIN3. Together, this work provides apowerful framework for the in vivo study of SIN3 and associated proteins.
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Programmed DNA elimination in Mesorhabditis nematodes
- Journal : Curr Biol
- 2023
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Cosegregation of recombinant chromatids maintains genome-wide heterozygosity in an asexual nematode
- Journal : Sci Adv
- 2023
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APOLLO, a testis-specific Drosophila ortholog of importin-4, mediates the loading of protamine-like protein Mst77F into sperm chromatin
- Journal : Journal of Biological Chemistry
- 2023
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Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.
- Journal : PLoS Comput Biol
- 2023
- In human and other metazoans, the determinants of replication origin location andstrength are still elusive. Origins are licensed in G1 phase and fired in S phaseof the cell cycle, respectively. It is debated which of these two temporallyseparate steps determines origin efficiency. Experiments can independentlyprofile mean replication timing (MRT) and replication fork directionality (RFD)genome-wide. Such profiles contain information on multiple origins' propertiesand on fork speed. Due to possible origin inactivation by passive replication,however, observed and intrinsic origin efficiencies can markedly differ. Thus,there is a need for methods to infer intrinsic from observed origin efficiency,which is context-dependent. Here, we show that MRT and RFD data are highlyconsistent with each other but contain information at different spatial scales.Using neural networks, we infer an origin licensing landscape that, when insertedin an appropriate simulation framework, jointly predicts MRT and RFD data withunprecedented precision and underlies the importance of dispersive origin firing.We furthermore uncover an analytical formula that predicts intrinsic fromobserved origin efficiency combined with MRT data. Comparison of inferredintrinsic origin efficiencies with experimental profiles of licensed origins(ORC, MCM) and actual initiation events (Bubble-seq, SNS-seq, OK-seq, ORM) showthat intrinsic origin efficiency is not solely determined by licensingefficiency. Thus, human replication origin efficiency is set at both the originlicensing and firing steps.
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HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.
- Journal : Proc Natl Acad Sci U S A
- 2023
- The spatial segregation of pericentromeric heterochromatin (PCH) into distinct,membrane-less nuclear compartments involves the binding of HeterochromatinProtein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibitsliquid-liquid phase separation properties in vitro, its mechanistic impact on thestructure and dynamics of PCH condensate formation in vivo remains largelyunresolved. Here, using a minimal theoretical framework, we systematicallyinvestigate the mutual coupling between self-interacting HP1-like molecules andthe chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3loci facilitates coacervation in nucleo and promotes the formation of stable PCHcondensates at HP1 levels far below the concentration required to observe phaseseparation in purified protein assays in vitro. These heterotypic HP1-chromatininteractions give rise to a strong dependence of the nucleoplasmic HP1 density onHP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponentphase separation. The dynamical cross talk between HP1 and the viscoelasticchromatin scaffold also leads to anomalously slow equilibration kinetics, whichstrongly depend on the genomic distribution of H3K9me2/3 domains and result inthe coexistence of multiple long-lived, microphase-separated PCH compartments.The morphology of these complex coacervates is further found to be governed bythe dynamic establishment of the underlying H3K9me2/3 landscape, which may drivetheir increasingly abnormal, aspherical shapes during cell development. Thesefindings compare favorably to 4D microscopy measurements of HP1 condensateformation in live Drosophila embryos and suggest a general quantitative model ofPCH formation based on the interplay between HP1-based phase separation andchromatin polymer mechanics.
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Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.
- Journal : Nat Commun
- 2023
- Spermiogenesis is a radical process of differentiation whereby sperm cellsacquire a compact and specialized morphology to cope with the constraints ofsexual reproduction while preserving their main cargo, an intact copy of thepaternal genome. In animals, this often involves the replacement of most histonesby sperm-specific nuclear basic proteins (SNBPs). Yet, how the SNBP-structuredgenome achieves compaction and accommodates shaping remain largely unknown. Here,we exploit confocal, electron and super-resolution microscopy, coupled withpolymer modeling to identify the higher-order architecture of sperm chromatin inthe needle-shaped nucleus of the emerging model cricket Gryllus bimaculatus.Accompanying spermatid differentiation, the SNBP-based genome is strikinglyreorganized as ~25nm-thick fibers orderly coiled along the elongated nucleusaxis. This chromatin spool is further found to achieve large-scale helicaltwisting in the final stages of spermiogenesis, favoring its ultracompaction. Wereveal that these dramatic transitions may be recapitulated by a surprisinglysimple biophysical principle based on a nucleated rigidification of chromatinlinked to the histone-to-SNBP transition within a confined nuclear space. Ourwork highlights a unique, liquid crystal-like mode of higher-order genomeorganization in ultracompact cricket sperm, and establishes a multidisciplinarymethodological framework to explore the diversity of non-canonical modes of DNAorganization.
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A burning question from the first international BPAN symposium: is restoration of autophagy a promising therapeutic strategy for BPAN?
- Journal : Autophagy
- 2023
- Beta-propeller protein-associated neurodegeneration (BPAN) is a rareneurodegenerative disease associated with severe cognitive and motor deficits.BPAN pathophysiology and phenotypic spectrum are still emerging due to the factthat mutations in the WDR45 (WD repeat domain 45) gene, a regulator ofmacroautophagy/autophagy, were only identified a decade ago. In the firstinternational symposium dedicated to BPAN, which was held in Lyon, France, apanel of international speakers, including several researchers from the autophagycommunity, presented their work on human patients, cellular and animal models,carrying WDR45 mutations and their homologs. Autophagy researchers found anopportunity to explore the defective function of autophagy mechanisms associatedwith WDR45 mutations, which underlie neuronal dysfunction and early death.Importantly, BPAN is one of the few human monogenic neurological diseasestargeting a regulator of autophagy, which raises the possibility that it is arelevant model to directly assess the roles of autophagy in neurodegeneration andto develop autophagy restorative therapeutic strategies for more commondisorders.
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Keeping Cell Death Alive: An Introduction into the French Cell Death Research Network.
- Journal : Biomolecules
- 2022
- Since the Nobel Prize award more than twenty years ago for discovering the coreapoptotic pathway in C. elegans, apoptosis and various other forms of regulatedcell death have been thoroughly characterized by researchers around the world.Although many aspects of regulated cell death still remain to be elucidated inspecific cell subtypes and disease conditions, many predicted that research intocell death was inexorably reaching a plateau. However, this was not the casesince the last decade saw a multitude of cell death modalities being described,while harnessing their therapeutic potential reached clinical use in certaincases. In line with keeping research into cell death alive, francophoneresearchers from several institutions in France and Belgium established theFrench Cell Death Research Network (FCDRN). The research conducted by FCDRN is atthe leading edge of emerging topics such as non-apoptotic functions of apoptoticeffectors, paracrine effects of cell death, novel canonical and non-canonicalmechanisms to induce apoptosis in cell death-resistant cancer cells or regulatedforms of necrosis and the associated immunogenic response. Collectively, thesevarious lines of research all emerged from the study of apoptosis and in the nextfew years will increase the mechanistic knowledge into regulated cell death andhow to harness it for therapy.
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Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability
- Journal : Genes and Development
- 2023
- Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans
- Journal : PLOS Biology
- 2023
- AMUeio: tPicledarsievceolnofcirimditshtaotratllthheeandoinrgmleavlelylseaqreuraelpsresgernetgedactioornreocftlayl:leles, which benefits their own transmission even in the face of severe fitness costs to their host organism. However, relatively little is known about the molecular identity of meiotic drivers, their strategies of action, and mechanisms that can suppress their activity. Here, we present data from the fruitfly Drosophila simulans that address these questions. We show that a family of de novo, protamine-derived X-linked selfish genes (the Dox gene family) is silenced by a pair of newly emerged hairpin RNA (hpRNA) small interfering RNA (siRNA)-class loci, Nmy and Tmy. In the w[XD1] genetic background, knockout of nmy derepresses Dox and MDox in testes and depletes male progeny, whereas knockout of tmy causes misexpression of PDox genes and renders males sterile. Importantly, genetic interactions between nmy and tmy mutant alleles reveal that Tmy also specifically maintains male progeny for normal sex ratio. We show the Dox loci are functionally polymorphic within D. simulans, such that both nmy-associated sex ratio bias and tmy-associated sterility can be rescued by wild-type X chromosomes bearing natural deletions in different Dox family genes. Finally, using tagged transgenes of Dox and PDox2, we provide the first experimental evidence Dox family genes encode proteins that are strongly derepressed in cognate hpRNA mutants. Altogether, these studies support a model in which protamine-derived drivers and hpRNA suppressors drive repeated cycles of sex chromosome conflict and resolution that shape genome evolution and the genetic control of male gametogenesis.
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Orientational Wetting and Topological Transitions in Confined Solutions of Semiflexible Polymers
- Journal : Macromolecules
- 2023
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4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling.
- Journal : Curr Opin Genet Dev
- 2023
- Recent experimental observations suggest a strong coupling between the 3D nuclearchromosome organization and epigenomics. However, the mechanistic and functionalbases of such interplay remain elusive. In this review, we describe howbiophysical modeling has been instrumental in characterizing how genome foldingmay impact the formation of epigenomic domains and, conversely, how epigenomicmarks may affect chromosome conformation. Finally, we discuss how this mutualfeedback loop between chromatin organization and epigenome regulation, via theformation of physicochemical nanoreactors, may represent a key functional role of3D compartmentalization in the assembly and maintenance of stable - but yetplastic - epigenomic landscapes.
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Cortisol Interaction with Aquaporin-2 Modulates Its Water Permeability: Perspectives for Non-Genomic Effects of Corticosteroids
- Journal : Int J Mol Sci
- 2023
Link to PubMed entry