Annuaire
2023
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Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation
- Journal : Biophysical Journal
- 2023
- The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent C⍺ model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.
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RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells.
- Journal : Nat Commun
- 2023
- Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitrythat coordinates gene expression at multiple levels from chromatin to mRNAprocessing. Recently, ribosome biogenesis and translation have emerged as keypathways that efficiently control stem cell homeostasis, yet the underlyingmolecular mechanisms remain largely unknown. Here, we identified RSL24D1 ashighly expressed in both mouse and human pluripotent stem cells. RSL24D1 isassociated with nuclear pre-ribosomes and is required for the biogenesis of 60Ssubunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairsglobal translation, particularly of key pluripotency factors and of componentsfrom the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact ondifferentiation, RSL24D1 depletion significantly alters ESC self-renewal andlineage commitment choices. Altogether, these results demonstrate thatRSL24D1-dependant ribosome biogenesis is both required to sustain the expressionof pluripotent transcriptional programs and to silence PRC2-regulateddevelopmental programs, which concertedly dictate ESC homeostasis.
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Severe COVID-19 patients have impaired plasmacytoid dendritic cell-mediated control of SARS-CoV-2.
- Journal : Nat Commun
- 2023
- Type I and III interferons (IFN-I/λ) are important antiviral mediators againstSARS-CoV-2 infection. Here, we demonstrate that plasmacytoid dendritic cells(pDC) are the predominant IFN-I/λ source following their sensing ofSARS-CoV-2-infected cells. Mechanistically, this short-range sensing by pDCsrequires sustained integrin-mediated cell adhesion with infected cells. In turn,pDCs restrict viral spread by an IFN-I/λ response directed towardSARS-CoV-2-infected cells. This specialized function enables pDCs to efficientlyturn-off viral replication, likely via a local response at the contact site withinfected cells. By exploring the pDC response in SARS-CoV-2 patients, we furtherdemonstrate that pDC responsiveness inversely correlates with the severity of thedisease. The pDC response is particularly impaired in severe COVID-19 patients.Overall, we propose that pDC activation is essential to controlSARS-CoV-2-infection. Failure to develop this response could be important tounderstand severe cases of COVID-19.
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Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
- Journal : Proteomics
- 2023
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Expulsion mechanism of the substrate-translocating subunit in ECF transporters
- Journal : Nature Communications
- 2023
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Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer
- Journal : Structure
- 2023
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An implementation of the Martini coarse-grained force field in OpenMM
- Journal : Biophysical Journal
- 2023
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Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface.
- Journal : J Mol Biol
- 2023
- The type VI secretion system (T6SS) is a multiprotein weapon evolved byGram-negative bacteria to deliver effectors into eukaryotic cells or bacterialrivals. The T6SS uses a contractile mechanism to propel an effector-loaded needleinto its target. The contractile tail is built on an assembly platform, thebaseplate, which is anchored to a membrane complex. Baseplate-membrane complexinteractions are mainly mediated by contacts between the C-terminal domain of theTssK baseplate component and the cytoplasmic domain of the TssL inner membraneprotein. Currently, the structural details of this interaction are unknown due tothe marginal stability of the TssK-TssL complex. Here we conducted a mutagenesisstudy based on putative TssK-TssL contact pairs identified by co-evolutionanalyses. We then evaluated the impact of these mutations on T6SS activity,TssK-TssL interaction and sheath assembly and dynamics in enteroaggregativeEscherichia coli. Finally, we probed the TssK-TssL interface by disulfidecross-linking, allowing to propose a model for the baseplate-membrane complexinterface.
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Acinetobacter type VI secretion system comprises a non-canonical membrane complex.
- Journal : PLoS Pathog
- 2023
- A. baumannii can rapidly acquire new resistance mechanisms and persist on abioticsurface, enabling the colonization of asymptomatic human host. In Acinetobacterthe type VI secretion system (T6SS) is involved in twitching, surface motilityand is used for interbacterial competition allowing the bacteria to uptake DNA.A. baumannii possesses a T6SS that has been well studied for its regulation andspecific activity, but little is known concerning its assembly and architecture.The T6SS nanomachine is built from three architectural sub-complexes. Unlike thebaseplate (BP) and the tail-tube complex (TTC), which are inherited frombacteriophages, the membrane complex (MC) originates from bacteria. The MC is themost external part of the T6SS and, as such, is subjected to evolution andadaptation. One unanswered question on the MC is how such a gigantesque molecularedifice is inserted and crosses the bacterial cell envelope. The A. baumannii MClacks an essential component, the TssJ lipoprotein, which anchors the MC to theouter membrane. In this work, we studied how A. baumannii compensates the absenceof a TssJ. We have characterized for the first time the A. baumannii's specificT6SS MC, its unique characteristic, its membrane localization, and assemblydynamics. We also defined its composition, demonstrating that its biogenesisemploys three Acinetobacter-specific envelope-associated proteins that define anintricate network leading to the assembly of a five-proteins membranesuper-complex. Our data suggest that A. baumannii has divided the function ofTssJ by (1) co-opting a new protein TsmK that stabilizes the MC and by (2)evolving a new domain in TssM for homo-oligomerization, a prerequisite to buildthe T6SS channel. We believe that the atypical species-specific features wereport in this study will have profound implication in our understanding of theassembly and evolutionary diversity of different T6SSs, that warrants futureinvestigation.
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Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity
- Journal : eLife
- 2023
- Here, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly accelerates BMT helped to illuminate the mechanism. Thus, incoming C/EBPα binds to PU.1, an obligate partner expressed in B cells, leading to the release of PU.1 from B cell enhancers, chromatin closing and silencing of the B cell program. Released PU.1 redistributes to macrophage enhancers newly occupied by C/EBPα, causing chromatin opening and activation of macrophage genes. All these steps are accelerated by C/EBPαR35A, initiated by its increased affinity for PU.1. Wild-type C/EBPα is methylated by Carm1 at arginine 35 and the enzyme’s perturbations modulate BMT velocity as predicted from the observations with the mutant. Increasing the proportion of unmethylated C/EBPα in granulocyte/macrophage progenitors by inhibiting Carm1 biases the cell’s differentiation toward macrophages, suggesting that cell fate decision velocity and lineage directionality are closely linked processes.
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Mechanism of homology search expansion during recombinational DNA break repair
- Journal : BioRxiv
- 2023
- Homology search catalyzed by a RecA/Rad51 nucleoprotein filament (NPF) is a central step of DNA double-strand break (DSB) repair by homologous recombination. How it operates in cells remains elusive. Here we developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short NPFs is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection by Exo1 drives this transition from local to genome-wide search by providing ssDNA substrates for assembly of extensive NPFs. DSB end-tethering promotes coordinated homology search by NPFs formed on the two DSB ends. Finally, an autonomous genetic element on chromosome III engages the NPF and stimulates homology search in its vicinity. This work reveals the mechanism of the progressive and uneven expansion of homology search orchestrated by chromatin organizers, long-range resection, end-tethering, specialized genetic elements, and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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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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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
- Journal : Journal of Chemical Theory and Computation
- 2023
- Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to biological membranes, switch their subcellular localization, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes including signal transduction, protein trafficking, and membrane localization and are implicated in various diseases as well. Examples of lipid-anchored proteins include the Ras family of proteins that undergo farnesylation; actin and gelsolin that are myristoylated; phospholipase D that is palmitoylated; glycosylphosphatidylinositol-anchored proteins; and others. Here, we develop parameters for cysteine-targeting farnesylation, geranylgeranylation, and palmitoylation, as well as glycine-targeting myristoylation for the latest version of the Martini 3 coarse-grained force field. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features of lipid-anchored peptides, such as the solvent-accessible surface area, bilayer penetration depth, and representative conformations of the anchors. The parameters are also validated in simulations of the lipid-anchored peripheral membrane proteins Rheb and Arf1, after comparison with independent all-atom simulations. The parameters, along with mapping schemes for the popular martinize2 tool, are available for download at 10.5281/zenodo.7849262 and also as supporting information.
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Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
- Journal : Communications biology
- 2023
- The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes. Here, we report on the identification of a promising class of inhibitors of the ECF transporters. We used coarse-grained molecular dynamics simulations on Lactobacillus delbrueckii ECF-FolT2 and ECF-PanT to profile the binding mode and mechanism of inhibition of this novel chemotype. The results corroborate the postulated mechanism of transport and pave the way for further drug-discovery efforts.
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CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization
- Journal : Journal of Chemical Theory and Computation
- 2023
- Coarse-grained force fields (CG FFs) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually all possible nonbonded interactions between chemically relevant molecules. Owing to its universality and transferability, the building-block coarse-grained approach has gained tremendous popularity over the past decade. The parametrization of molecules can be highly complex and often involves the selection and fine-tuning of a large number of parameters (e.g., bead types and bond lengths) to optimally match multiple relevant targets simultaneously. The parametrization of a molecule within the building-block CG approach is a mixed-variable optimization problem: the nonbonded interactions are discrete variables, whereas the bonded interactions are continuous variables. Here, we pioneer the utility of mixed-variable particle swarm optimization in automatically parametrizing molecules within the Martini 3 coarse-grained force field by matching both structural (e.g., RDFs) as well as thermodynamic data (phase-transition temperatures). For the sake of demonstration, we parametrize the linker of the lipid sphingomyelin. The important advantage of our approach is that both bonded and nonbonded interactions are simultaneously optimized while conserving the search efficiency of vector guided particle swarm optimization (PSO) methods over other metaheuristic search methods such as genetic algorithms. In addition, we explore noise-mitigation strategies in matching the phase-transition temperatures of lipid membranes, where nucleation and concomitant hysteresis introduce a dominant noise term within the objective function. We propose that noise-resistant mixed-variable PSO methods can both improve and automate parametrization of molecules within building-block CG FFs, such as Martini.
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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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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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Martini 3 Coarse-Grained Force Field for Cholesterol
- Journal : Journal of Chemical Theory and Computation
- 2023
- Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
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Pragmatic Coarse-Graining of Proteins: Models and Applications
- Journal : Journal of Chemical Theory and Computation
- 2023
- The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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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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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.
Link to PubMed entry