Skip to content. | Skip to navigation

Personal tools

You are here: Home / Publications / Publications


The last 50 bibliographies

APOLLO, a testis-specific Drosophila ortholog of importin-4, mediates the loading of protamine-like protein Mst77F into sperm chromatin

Author(s) : Emelyanov A, Barcenilla-Merino D, Loppin B, Fyodorov D,
Journal : Journal of Biological Chemistry

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.

Author(s) : Arbona J, Kabalane H, Barbier J, Goldar A, Hyrien O, Audit B,
Journal : PLoS Comput Biol
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.

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.

Author(s) : Tortora M, Brennan L, Karpen G, Jost D,
Journal : Proc Natl Acad Sci U S A
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.

Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.

Author(s) : Orsi G, Tortora M, Horard B, Baas D, Kleman J, Bucevičius J, Lukinavičius G, Jost D, Loppin B,
Journal : Nat Commun
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.

A burning question from the first international BPAN symposium: is restoration of autophagy a promising therapeutic strategy for BPAN?

Author(s) : Mollereau B, Hayflick S, Escalante R, Mauthe M, Papandreou A, Iuso A, Celle M, Aniorte S, Issa A, Lasserre J, Lesca G, Thobois S, Burger P, Walter L,
Journal : Autophagy
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.

Keeping Cell Death Alive: An Introduction into the French Cell Death Research Network.

Author(s) : Ichim G, Gibert B, Adriouch S, Brenner C, Davoust N, Desagher S, Devos D, Dokudovskaya S, Dubrez L, Estaquier J, Gillet G, Guénal I, Juin P, Kroemer G, Legembre P, Levayer R, Manon S, Mehlen P, Meurette O, Micheau O, Mignotte B, Nguyen-Khac F, Popgeorgiev N, Poyet J, Priault M, Ricci J, Riquet F, Susin S, Suzanne M, Vacher P, Walter L, Mollereau B,
Journal : Biomolecules
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.

Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability

Author(s) : Reitz D, Djeghmoum Y, Piazza A,
Journal : Genes and Development
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.

Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans

Author(s) : Vedanayagam J, Herbette M, Mudgett H, Lin C, Lai C, McDonough-Goldstein C, Dorus S, Loppin B, Meiklejohn C, Dubruille R, Lai E,
Journal : PLOS Biology
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.

Orientational Wetting and Topological Transitions in Confined Solutions of Semiflexible Polymers

Author(s) : Tortora M, Jost D,
Journal : Macromolecules

4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling.

Author(s) : Abdulla A, Salari H, Tortora M, Vaillant C, Jost D,
Journal : Curr Opin Genet Dev
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.

SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans

Author(s) : Caron M, Robert V, Gely L, Adrait A, Pakulska V, Couté Y, Chevalier M, Riedel C, Bedet C, Palladino F,
Journal : bioRxiv
The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here we show that loss of SIN-3, the single SIN3 homologue in Caenorhabditis elegans, results in maternal effect sterility associated with deregulation of the germline transcriptome, including desilencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific HDACs, and show that they differentially contribute to fertility. Single cell smFISH reveals that in sin-3 mutants, the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins.Competing Interest StatementThe authors have declared no competing interest.

Cortisol Interaction with Aquaporin-2 Modulates Its Water Permeability: Perspectives for Non-Genomic Effects of Corticosteroids

Author(s) : Mom R, Réty S, Auguin D,
Journal : Int J Mol Sci

Structural Studies of Pif1 Helicases from Thermophilic Bacteria

Author(s) : Réty S, Zhang Y, Fu W, Wang S, Chen W, Xi X,
Journal : Microorganisms

Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms

Author(s) : Louro J, Boopathi R, Beinsteiner B, Mohideen Patel A, Cheng T, Angelov D, Hamiche A, Bendar J, Kale S, Klaholz B, Dimitrov S,
Journal : Structure

Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities

Author(s) : Song Q, Liu N, Liu Z, Zhang Y, Rety S, Hou X, Xi X,
Journal : J Biol Chem

One model fits all: Combining inference and simulation of gene regulatory networks

Author(s) : Ventre E, Herbach U, Espinasse T, Benoit G, Gandrillon O,
Journal : PLoS Comput Biol

Functional analysis of Wolbachia Cid effectors unravels cooperative interactions to target host chromatin during replication

Author(s) : Terretaz K, Horard B, Weill M, Loppin B, Landmann F,
Journal : PLOS Pathogens
Wolbachia are common bacteria among terrestrial arthropods. These endosymbionts transmitted through the female germline manipulate their host reproduction through several mechanisms whose most prevalent form called Cytoplasmic Incompatibility -CI- is a conditional sterility syndrome eventually favoring the infected progeny. Upon fertilization, the sperm derived from an infected male is only compatible with an egg harboring a compatible Wolbachia strain, this sperm leading otherwise to embryonic death. The Wolbachia Cif factors CidA and CidB responsible for CI and its neutralization function as a Toxin-Antitoxin system in the mosquito host Culex pipiens . However, the mechanism of CidB toxicity and its neutralization by the CidA antitoxin remain unexplored. Using transfected insect cell lines to perform a structure-function analysis of these effectors, we show that both CidA and CidB are chromatin interactors and CidA anchors CidB to the chromatin in a cell-cycle dependent-manner. In absence of CidA, the CidB toxin localizes to its own chromatin microenvironment and acts by preventing S-phase completion, independently of its deubiquitylase -DUB- domain. Experiments with transgenic Drosophila show that CidB DUB domain is required together with CidA during spermatogenesis to stabilize the CidA-CidB complex. Our study defines CidB functional regions and paves the way to elucidate the mechanism of its toxicity.

The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling

Author(s) : Plana-Carmona M, Stik G, Bulteau R, Segura-Morales C, Alcázar N, Wyatt C, Klonizakis A, de Andrés-Aguayo L, Gasnier M, Tian T, Torcal Garcia G, Vila-Casadesús M, Plachta N, Serrano M, Francesconi M, Graf T,
Journal : Stem Cell Reports
IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how Il6 expression is regulated and whether it plays a role during embryo development remains unknown. Here, we describe that IL-6 is necessary for C/EBPα-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPα overexpression activates both Il6 and Il6ra genes in B cells and in PSCs. In embryo development, Cebpa is enriched in the trophectoderm of blastocysts together with Il6, while Il6ra is mostly expressed in the inner cell mass (ICM). In addition, Il6 expression in blastocysts requires Cebpa. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. The observed requirement of C/EBPα-regulated IL-6 signaling for pluripotency during somatic cell reprogramming thus recapitulates a physiologic mechanism in which the trophectoderm acts as niche for the ICM through the secretion of IL-6.

Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.

Author(s) : Parmentier R, Racine L, Moussy A, Chantalat S, Sudharshan R, Papili Gao N, Stockholm D, Corre G, Fourel G, Deleuze J, Gunawan R, Paldi A,
Journal : PLoS Biol
When human cord blood-derived CD34+ cells are induced to differentiate, theyundergo rapid and dynamic morphological and molecular transformations that arecritical for fate commitment. In particular, the cells pass through a transitoryphase known as "multilineage-primed" state. These cells are characterized by amixed gene expression profile, different in each cell, with the coexpression ofmany genes characteristic for concurrent cell lineages. The aim of our study isto understand the mechanisms of the establishment and the exit from thistransitory state. We investigated this issue using single-cell RNA sequencing andATAC-seq. Two phases were detected. The first phase is a rapid and globalchromatin decompaction that makes most of the gene promoters in the genomeaccessible for transcription. It results 24 h later in enhanced and pervasivetranscription of the genome leading to the concomitant increase in thecell-to-cell variability of transcriptional profiles. The second phase is theexit from the multilineage-primed phase marked by a slow chromatin closure and asubsequent overall down-regulation of gene transcription. This process isselective and results in the emergence of coherent expression profilescorresponding to distinct cell subpopulations. The typical time scale of theseevents spans 48 to 72 h. These observations suggest that the nonspecificity ofgenome decompaction is the condition for the generation of a highly variablemultilineage expression profile. The nonspecific phase is followed by specificregulatory actions that stabilize and maintain the activity of key genes, whilethe rest of the genome becomes repressed again by the chromatin recompaction.Thus, the initiation of differentiation is reminiscent of a constrainedoptimization process that associates the spontaneous generation of geneexpression diversity to subsequent regulatory actions that maintain the activityof some genes, while the rest of the genome sinks back to the repressive closedchromatin state.