Nous étudions la dynamique de la chromatine dans le cadre de la réplication chez le myxomycète Physarum polycephalum.
Notre équipe utilise les caractéristiques uniques du myxomycète Physarum polycephalum, communément connu sous le nom de Blob, afin d’étudier la dynamique de la chromatine lors de la réplication. En effet, ce modèle original présente une synchronie parfaite de plusieurs centaines de millions de noyaux contenus dans une cellule géante appelée plasmode. De plus, le Blob a la capacité d’internaliser et d’utiliser des protéines exogènes. Depuis plusieurs années, nous avons étudié les régions des histones nécessaires au transport nucléaire et à l’assemblage en chromatine pendant la phase S du cycle cellulaire. Grâce à l’accès au génome de Physarum depuis 2016, nous développons à présent des approches de génomique – notamment de CUT&RUN – afin d’analyser le rétablissement de la structure de la chromatine après réplication de l’ADN. Nous avons également initié des approches génétiques chez Physarum, aucun outil ou ressource génétique n’étant disponible à ce jour. Notre but est d’être en mesure de transformer Physarum sous sa forme diploïde par les techniques de biolistique. Enfin, outre nos travaux chez Physarum, nous menons des approches biochimiques afin de définir in vitro les altérations de la structure d’un modèle de chromatine sous l’influence de l’histone centromérique CENP-A.
@article{ijms22031113,
title = {Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication},
author = {Céline Duc and Christophe Thiriet},
url = {https://www.mdpi.com/1422-0067/22/3/1113},
doi = {10.3390/ijms22031113},
issn = {1422-0067},
year = {2021},
date = {2021-01-01},
journal = {International Journal of Molecular Sciences},
volume = {22},
number = {3},
abstract = {The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.
@article{duc_trapping_2019,
title = {Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion},
author = {Céline Duc and Marianne Yoth and Silke Jensen and Nolwenn Mouniée and Casey M Bergman and Chantal Vaury and Emilie Brasset},
url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1736-x},
doi = {10.1186/s13059-019-1736-x},
issn = {1474-760X},
year = {2019},
date = {2019-01-01},
urldate = {2021-02-25},
journal = {Genome Biology},
volume = {20},
number = {1},
pages = {127},
abstract = {Background: For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion.
Results: To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.
Conclusions: Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of a germline endangered by mobilization of a surrounding somatic TE.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion.
Results: To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.
Conclusions: Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of a germline endangered by mobilization of a surrounding somatic TE.
@incollection{cEQ4:THIRIET:2018,
title = {Nuclear Dynamics at Specific Cell Cycle Stages in the Slime Mold emphPhysarum polycephalum},
author = {Christophe Thiriet},
editor = {Christophe Lavelle and Jean-Marc Victor},
url = {http://www.sciencedirect.com/science/article/pii/B9780128034804000247},
doi = {https://doi.org/10.1016/B978-0-12-803480-4.00024-7},
issn = {25425358},
year = {2018},
date = {2018-01-01},
booktitle = {Nuclear Architecture and Dynamics},
volume = {2},
pages = {557 - 567},
publisher = {Academic Press},
address = {Boston},
series = {Translational Epigenetics},
abstract = {The genetic activities require the alteration of chromatin structures. This involves movements of nucleosomes that make accessible the genetic information. Understanding the mechanisms of chromatin activities, the roles of histone domains and modifications in vivo are important tasks. The slime mold Physarum polycephalum is a powerful model system with millions of naturally synchronous nuclei and the unique capability to spontaneously internalize exogenous proteins. The present chapter describes the life cycle of the myxomycete and provides examples of analyses of chromatin dynamics in replication and in transcription.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
The genetic activities require the alteration of chromatin structures. This involves movements of nucleosomes that make accessible the genetic information. Understanding the mechanisms of chromatin activities, the roles of histone domains and modifications in vivo are important tasks. The slime mold Physarum polycephalum is a powerful model system with millions of naturally synchronous nuclei and the unique capability to spontaneously internalize exogenous proteins. The present chapter describes the life cycle of the myxomycete and provides examples of analyses of chromatin dynamics in replication and in transcription.
@article{Ejlassi2017b,
title = {Histones H3 and H4 require their relevant amino-tails for efficient nuclear import and replication-coupled chromatin assembly in vivo},
author = {Aïda Ejlassi and Vanessa Menil-Philippot and Angélique Galvani and Christophe Thiriet},
doi = {10.1038/s41598-017-03218-6},
issn = {20452322},
year = {2017},
date = {2017-01-01},
journal = {Scientific Reports},
volume = {7},
number = {1},
pages = {1--10},
abstract = {Concomitant chromatin assembly and DNA duplication is essential for cell survival and genome integrity, and requires newly synthesized histones. Although the N-terminal domains of newly synthesized H3 and H4 present critical functions, their requirement for replication-coupled chromatin assembly is controversial. Using the unique capability of the spontaneous internalization of exogenous proteins in Physarum, we showed that H3 and H4 N-tails present critical functions in nuclear import during the S-phase, but are dispensable for assembly into nucleosomes. However, our data revealed that chromatin assembly in the S-phase of complexes presenting ectopic N-terminal domains occurs by a replication-independent mechanism. We found that replication-dependent chromatin assembly requires an H3/H4 complex with the relevant N-tail domains, suggesting a concomitant recognition of the two histone domains by histone chaperones.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Concomitant chromatin assembly and DNA duplication is essential for cell survival and genome integrity, and requires newly synthesized histones. Although the N-terminal domains of newly synthesized H3 and H4 present critical functions, their requirement for replication-coupled chromatin assembly is controversial. Using the unique capability of the spontaneous internalization of exogenous proteins in Physarum, we showed that H3 and H4 N-tails present critical functions in nuclear import during the S-phase, but are dispensable for assembly into nucleosomes. However, our data revealed that chromatin assembly in the S-phase of complexes presenting ectopic N-terminal domains occurs by a replication-independent mechanism. We found that replication-dependent chromatin assembly requires an H3/H4 complex with the relevant N-tail domains, suggesting a concomitant recognition of the two histone domains by histone chaperones.
@article{Menil-Philippot2017,
title = {Physarum polycephalum for Studying the Function of Histone Modifications In Vivo.},
author = {Vanessa Menil-Philippot and Christophe Thiriet},
doi = {10.1007/978-1-4939-6630-1_15},
issn = {1940-6029 (Electronic)},
year = {2017},
date = {2017-01-01},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1528},
pages = {245--256},
abstract = {Histone modifications have been widely correlated with genetic activities. However, how these posttranslational modifications affect the dynamics and the structure of chromatin is poorly understood. Here, we describe the incorporation of the exogenous histone proteins into the slime mold Physarum polycephalum, which has been revealed to be a valuable tool for examining different facets of the function histones in chromatin dynamics like replication-coupled chromatin assembly, histone exchange, and nucleosome turnover.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Histone modifications have been widely correlated with genetic activities. However, how these posttranslational modifications affect the dynamics and the structure of chromatin is poorly understood. Here, we describe the incorporation of the exogenous histone proteins into the slime mold Physarum polycephalum, which has been revealed to be a valuable tool for examining different facets of the function histones in chromatin dynamics like replication-coupled chromatin assembly, histone exchange, and nucleosome turnover.
@article{Rouaud2017,
title = {Complement C3 of the innate immune system secreted by muscle adipogenic cells promotes myogenic differentiation},
author = {Thierry Rouaud and Nader Siami and Tanaelle Dupas and Pascal Gervier and Marie France Gardahaut and Gwenola Auda-Boucher and Christophe Thiriet},
doi = {10.1038/s41598-017-00099-7},
issn = {20452322},
year = {2017},
date = {2017-01-01},
journal = {Scientific Reports},
volume = {7},
number = {1},
pages = {1--9},
abstract = {Myogenic differentiation results in different cell type cooperation, but the molecules involved in the myogenic cell activation remain elusive. Here, we show that muscle-resident pre-adipocytes promote myogenic differentiation through the secretion of factors. Using proteomic and transcriptomic analyses, we identified that proliferative adipogenic lineage cells produce and secrete a key factor of the innate immune system, the complement C3. Cell culture experiments revealed that C3 promotes the differentiation of myogenic progenitors following internalisation of the immune molecule. These data demonstrate that the third component of the complement system, which is a pivotal factor in the immune response to pathogens, is also involved in the differentiation of myogenic progenitor cells.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Myogenic differentiation results in different cell type cooperation, but the molecules involved in the myogenic cell activation remain elusive. Here, we show that muscle-resident pre-adipocytes promote myogenic differentiation through the secretion of factors. Using proteomic and transcriptomic analyses, we identified that proliferative adipogenic lineage cells produce and secrete a key factor of the innate immune system, the complement C3. Cell culture experiments revealed that C3 promotes the differentiation of myogenic progenitors following internalisation of the immune molecule. These data demonstrate that the third component of the complement system, which is a pivotal factor in the immune response to pathogens, is also involved in the differentiation of myogenic progenitor cells.
@article{rEQ4:THIRIET:2015,
title = {Nucleosome Dancing at the Tempo of Histone Tail Acetylation},
author = {Angélique Galvani and Christophe Thiriet},
url = {https://doi.org/10.3390/genes6030607},
doi = {10.3390/genes6030607},
year = {2015},
date = {2015-07-01},
journal = {Genes (Basel)},
volume = {6},
number = {3},
pages = {607-21},
abstract = {The impact of histone acetylation on transcription was revealed over 50 years ago by Allfrey and colleagues. However, it took decades for an understanding of the fine mechanism by which this posttranslational modification affects chromatin structure and promotes transcription. Here, we review breakthroughs linking histone tail acetylation, histone dynamics, and transcription. We also discuss the histone exchange during transcription and highlight the important function of a pool of non-chromatinized histones in chromatin dynamics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The impact of histone acetylation on transcription was revealed over 50 years ago by Allfrey and colleagues. However, it took decades for an understanding of the fine mechanism by which this posttranslational modification affects chromatin structure and promotes transcription. Here, we review breakthroughs linking histone tail acetylation, histone dynamics, and transcription. We also discuss the histone exchange during transcription and highlight the important function of a pool of non-chromatinized histones in chromatin dynamics.
