@article{nokey,

title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems},

author = {France Denoeud and Olivier Godfroy and Corinne Cruaud and Svenja Heesch and Zofia Nehr and Nachida Tadrent and Arnaud Couloux and Loraine Brillet-Guéguen and Ludovic Delage and Dean Mckeown and Taizo Motomura and Duncan Sussfeld and Xiao Fan 0and Lisa Mazéas and Nicolas Terrapon and Josué Barrera-Redondo and Romy Petroll and Lauric Reynes and Seok-Wan Choi and Jihoon Jo and Kavitha Uthanumallian and Kenny Bogaert and Céline Duc and Pélagie Ratchinski and Agnieszka Lipinska and Benjamin Noel and Eleanor A Murphy and Martin Lohr 0and Ananya Khatei and Pauline Hamon-Giraud and Christophe Vieira and Komlan Avia and Svea Sanja Akerfors 0and Shingo Akita and Yacine Badis and Tristan Barbeyron and Arnaud Belcour and Wahiba Berrabah and Samuel Blanquart and Ahlem Bouguerba-Collin and Trevor Bringloe and Rose Ann Cattolico and Alexandre Cormier and Helena Cruz de Carvalho and Romain Dallet and Olivier De Clerck and Ahmed Debit and Erwan Denis and Christophe Destombe and Erica Dinatale and Simon Dittami and Elodie Drula and Sylvain Faugeron 0and Jeanne Got and Louis Graf and Agnès Groisillier and Marie-Laure Guillemin and Lars Harms and William John Hatchett and Bernard Henrissat and Galice Hoarau and Chloé Jollivet and Alexander Jueterbock and Ehsan Kayal and Andrew H Knoll and Kazuhiro Kogame and Arthur Le Bars and Catherine Leblanc and Line Le Gall and Ronja Ley 0and Xi Liu and Steven T LoDuca and Pascal Jean Lopez 0and Philippe Lopez and Eric Manirakiza and Karine Massau and Stéphane Mauger and Laetitia Mest and Gurvan Michel and Catia Monteiro and Chikako Nagasato and Delphine Nègre and Eric Pelletier and Naomi Phillips and Philippe Potin and Stefan A Rensing and Ellyn Rousselot and Sylvie Rousvoal and Declan Schroeder and Delphine Scornet and Anne Siegel and Leila Tirichine and Thierry Tonon and Klaus Valentin and Heroen Verbruggen and Florian Weinberger and Glen Wheeler and Hiroshi Kawai and Akira F Peters and Hwan Su Yoon and Cécile Hervé 0and Naihao Ye and Eric Bapteste and Myriam Valero and Gabriel V Markov and Erwan Corre and Susana M Coelho and Patrick Wincker and Jean-Marc Aury and J Mark Cock },

editor = {Cell Press},

url = {https://www.cell.com/cell/fulltext/S0092-8674(24)01272-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867424012728%3Fshowall%3Dtrue},

doi = {doi: 10.1016/j.cell.2024.10.049},

year  = {2024},

date = {2024-11-27},

journal = {Cell},

volume = {187},

issue = {24},

pages = {6943-6965},

abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {H3K27me3 and EZH Are Involved in the Control of the Heat-Stress-Elicited Morphological Changes in Diatoms},

author = {Mhammad Zarif and Ellyn Rousselot and Bruno Jesus and Leïla Tirichine and Céline Duc},

editor = {MDPI},

url = {https://www.mdpi.com/1422-0067/25/15/8373},

doi = {doi.org/10.3390/ijms25158373},

year  = {2024},

date = {2024-07-31},

journal = {Int. J. Mol. Sci.},

volume = {25},

issue = {15},

pages = {8373},

abstract = {Marine water temperatures are increasing due to anthropogenic climate change, constituting a major threat to marine ecosystems. Diatoms are major marine primary producers, and as such, they are subjected to marine heat waves and rising ocean temperatures. Additionally, under low tide, diatoms are regularly exposed to high temperatures. However, physiological and epigenetic responses to long-term exposure to heat stress remain largely unknown in the diatom Phaeodactylum tricornutum. In this study, we investigated changes in cell morphology, photosynthesis, and H3K27me3 abundance (an epigenetic mark consisting of the tri-methylation of lysine 27 on histone H3) after moderate and elevated heat stresses. Mutants impaired in PtEZH—the enzyme depositing H3K27me3—presented reduced growth and moderate changes in their PSII quantum capacities. We observed shape changes for the three morphotypes of P. tricornutum (fusiform, oval, and triradiate) in response to heat stress. These changes were found to be under the control of PtEZH. Additionally, both moderate and elevated heat stresses modulated the expression of genes encoding proteins involved in photosynthesis. Finally, heat stress elicited a reduction of genome-wide H3K27me3 levels in the various morphotypes. Hence, we provided direct evidence of epigenetic control of the H3K27me3 mark in the responses of Phaeodactylum tricornutum to heat stress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms24021051,

title = {The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum},

author = {Axel Poulet and Ellyn Rousselot and Stéphane Téletchéa and Céline Noirot and Yannick Jacob and Josien Wolfswinkel and Christophe Thiriet and Céline Duc},

url = {https://www.mdpi.com/1422-0067/24/2/1051

 hal-03978828v1 },

doi = {10.3390/ijms24021051},

issn = {1422-0067},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {International Journal of Molecular Sciences},

volume = {24},

number = {2},

abstract = {The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/nargab/lqab107,

title = {Identification and characterization of histones in Physarum polycephalum evidence a phylogenetic vicinity of Mycetozoans to the animal kingdom},

author = {Axel Poulet and Laxmi Narayan Mishra and Stéphane Téletchéa and Jeffrey J Hayes and Yannick Jacob and Christophe Thiriet and Céline Duc},

url = {https://doi.org/10.1093/nargab/lqab107

hal-03595485v1 },

doi = {10.1093/nargab/lqab107},

issn = {2631-9268},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {NAR Genomics and Bioinformatics},

volume = {3},

number = {4},

abstract = {Physarum polycephalum belongs to Mycetozoans, a phylogenetic clade apart from the animal, plant and fungus kingdoms. Histones are nuclear proteins involved in genome organization and regulation and are among the most evolutionary conserved proteins within eukaryotes. Therefore, this raises the question of their conservation in Physarum and the position of this organism within the eukaryotic phylogenic tree based on histone sequences. We carried out a comprehensive study of histones in Physarum polycephalum using genomic, transcriptomic and molecular data. Our results allowed to identify the different isoforms of the core histones H2A, H2B, H3 and H4 which exhibit strong conservation of amino acid residues previously identified as subject to post-translational modifications. Furthermore, we also identified the linker histone H1, the most divergent histone, and characterized a large number of its PTMs by mass spectrometry. We also performed an in-depth investigation of histone genes and transcript structures. Histone proteins are highly conserved in Physarum and their characterization will contribute to a better understanding of the polyphyletic Mycetozoan group. Our data reinforce that P. polycephalum is evolutionary closer to animals than plants and located at the crown of the eukaryotic tree. Our study provides new insights in the evolutionary history of Physarum and eukaryote lineages.},

note = {lqab107},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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

hal-04210949v1 },

doi = {10.3390/ijms22031113},

issn = {1422-0067},

year  = {2021},

date = {2021-01-01},

urldate = {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}

}

@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 = {2019-01-01},

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}

}