Profitez de la vie comme si c'est le dernier jour et faites des projets comme si elle était éternelle

Leila TIRICHINE
Directrice de recherche CNRS
section 23
Équipe : |
Thèmes de recherche
Mécanismes moléculaires des interactions micro-algues facteurs biotiques et abiotiques de l’environnement, Biotechnologies, Bio-informatique
Projets
Parcours universitaire
2018 – DU bioinformatique Université Paris Diderot
2000 – Doctorat en Biologie Moléculaire et Cellulaire, INP Toulouse
1996 – DEA en génétique Quantitative et Amélioration des Plantes, ENSA Rennes
1995 – Diplôme d’ingénieur Agronome ENSA Toulouse
Publications
3 publications
Hoguin, Antoine; Yang, Feng; Groisillier, Agnès; Bowler, Chris; Genovesio, Auguste; Ait-Mohamed, Ouardia; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases Article de journal
Dans: Communications Biology, vol. 6, iss. 1, no. 1, p. 253, 2023, ISSN: 23993642.
@article{Hoguin2023,
title = {The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases},
author = {Antoine Hoguin and Feng Yang and Agnès Groisillier and Chris Bowler and Auguste Genovesio and Ouardia Ait-Mohamed and Fabio Rocha Jimenez Vieira and Leila Tirichine},
editor = {Nature},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9998398/},
doi = {10.1038/s42003-023-04629-0 },
issn = {23993642},
year = {2023},
date = {2023-03-09},
urldate = {2023-03-09},
journal = {Communications Biology},
volume = {6},
number = {1},
issue = {1},
pages = {253},
abstract = {Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tirichine, Leila; Piganeau, Gwenael
Editorial: Algal symbiotic relationships in freshwater and marine environments Article de journal
Dans: Front. Plant Sci., 2023.
@article{nokey,
title = {Editorial: Algal symbiotic relationships in freshwater and marine environments},
author = {Leila Tirichine and Gwenael Piganeau},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1155759/full},
doi = {doi: 10.3389/fpls.2023.1155759},
year = {2023},
date = {2023-02-20},
urldate = {2023-02-20},
journal = {Front. Plant Sci.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shao, Zhanru; andFabio Vieira, Osei Ampomah; Dorrell, Richard; Li, Shaoxuan; Tirichine, Leila; Bulone, Vincent; Duan, Delin; Bowler, Chris
Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. Article de journal
Dans: mSystems, 2023.
@article{nokey,
title = {Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. },
author = {Zhanru Shao and Osei Ampomah andFabio Vieira and Richard Dorrell and Shaoxuan Li and Leila Tirichine and Vincent Bulone and Delin Duan and Chris Bowler},
doi = {doi: 10.1128/msystems.01131-22},
year = {2023},
date = {2023-02-15},
urldate = {2023-02-15},
journal = {mSystems},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
5 publications
Chandola, Udita; Trottier, Camille; Gaudin, Marinna; Manirakiza, Erik; Menicot, Samuel; Louvet, Isabelle; Lacour, Thomas; Chaumier, Timothée; Tanaka, Atsuko; Chaffron, Samuel; Tirichine, Leila
Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Chandola2022.08.25.505241,
title = {Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae},
author = {Udita Chandola and Camille Trottier and Marinna Gaudin and Erik Manirakiza and Samuel Menicot and Isabelle Louvet and Thomas Lacour and Timothée Chaumier and Atsuko Tanaka and Samuel Chaffron and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/25/2022.08.25.505241},
doi = {10.1101/2022.08.25.505241},
year = {2022},
date = {2022-08-25},
urldate = {2022-08-25},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum (Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified PtNCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in PtNCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Wu, Yue; Timothée, Chaumier; Manirakiza, Eric; Veluchamy, Alaguraj; Tirichine, Leila
PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Wu2022.07.29.502047,
title = {PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},
author = {Yue Wu and Chaumier Timothée and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/01/2022.07.29.502047},
doi = {10.1101/2022.07.29.502047},
year = {2022},
date = {2022-08-01},
urldate = {2022-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Motivation Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research.Results Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice.Availability PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.frCompeting Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leila
Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies Chapitre d'ouvrage
Dans: Falciatore, Angela; Mock, Thomas (Ed.): The Molecular Life of Diatoms, p. 179–202, Springer International Publishing, Cham, 2022, ISBN: 978-3-030-92499-7.
@inbook{Zhao2022,
title = {Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies},
author = {Xue Zhao and Antoine Hoguin and Timothée Chaumier and Leila Tirichine},
editor = {Angela Falciatore and Thomas Mock},
url = {https://doi.org/10.1007/978-3-030-92499-7_7},
doi = {10.1007/978-3-030-92499-7_7},
isbn = {978-3-030-92499-7},
year = {2022},
date = {2022-05-12},
urldate = {2022-01-01},
booktitle = {The Molecular Life of Diatoms},
pages = {179--202},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {Epigenetics and its role in genome regulation is one of the most exciting areas of modern science. After a brief history of epigenetics and an introduction to the molecular basics of this discipline of science, this chapter describes the current knowledge of epigenetic components in diatoms, namely writers and erasers of DNA methylation and histone modifications. With a particular focus on the model pennate diatom Phaeodactylum tricornutum, we describe our current understanding of the contribution of few epigenetic factors to diatoms biology. Further, short regulatory non-coding RNAs (ncRNAs) as well as long ncRNAs are described in light of recent research. We highlight future studies and directions with a focus on epigenomic editing and environmental epigenetics.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Bourdareau, Simon; Godfroy, Olivier; Gueno, Josselin; Scornet, Delphine; Coelho, Susana M.; Tirichine, Leila; Cock, Jean Mark
An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus Article de journal
Dans: Methods Protoc. , vol. 36, iss. 3, p. 36, 2022.
@article{nokey,
title = {An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus},
author = {Simon Bourdareau and Olivier Godfroy and Josselin Gueno and Delphine Scornet and Susana M. Coelho and Leila Tirichine and Jean Mark Cock},
doi = {doi: 10.3390/mps5030036},
year = {2022},
date = {2022-04-25},
urldate = {2022-04-25},
journal = {Methods Protoc. },
volume = {36},
issue = {3},
pages = {36},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gueno, Josselin; Borg, Michael; Bourdareau, Simon; Cossard, Guillaume; Godfroy, Olivier; Lipinska, Agnieszka; Tirichine, Leila; Cock, J Mark; Coelho, Susana M
Chromatin landscape associated with sexual differentiation in a UV sex determination system Article de journal
Dans: Nucleic Acids Res, vol. 50, iss. 6, p. 3307-3322, 2022, ISSN: 1362-4962.
@article{pmid35253891,
title = {Chromatin landscape associated with sexual differentiation in a UV sex determination system},
author = {Josselin Gueno and Michael Borg and Simon Bourdareau and Guillaume Cossard and Olivier Godfroy and Agnieszka Lipinska and Leila Tirichine and J Mark Cock and Susana M Coelho},
doi = {doi: 10.1093/nar/gkac145},
issn = {1362-4962},
year = {2022},
date = {2022-03-01},
urldate = {2022-03-01},
journal = {Nucleic Acids Res},
volume = {50},
issue = {6},
pages = {3307-3322},
abstract = {In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
5 publications
Bourdareau, Simon; Tirichine, Leila; Lombard, Bérangère; Loew, Damarys; Scornet, Delphine; Wu, Yue; Coelho, Susana M; Cock, Mark J
Histone modifications during the life cycle of the brown alga Ectocarpus Article de journal
Dans: Genome Biology, vol. 22, no. 1, 2021, ISSN: 1474760X.
@article{Bourdareau2021,
title = {Histone modifications during the life cycle of the brown alga Ectocarpus},
author = {Simon Bourdareau and Leila Tirichine and Bérangère Lombard and Damarys Loew and Delphine Scornet and Yue Wu and Susana M Coelho and Mark J Cock},
url = {https://pubmed.ncbi.nlm.nih.gov/33397407/},
doi = {10.1186/s13059-020-02216-8},
issn = {1474760X},
year = {2021},
date = {2021-12-01},
journal = {Genome Biology},
volume = {22},
number = {1},
publisher = {BioMed Central Ltd},
abstract = {Background: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoguin, Antoine; Rastogi, Achal; Bowler, Chris; Tirichine, Leila
Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum Article de journal
Dans: Scientific Reports, p. 1–10, 2021, ISSN: 2045-2322.
@article{Hoguin2021,
title = {Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum},
author = {Antoine Hoguin and Achal Rastogi and Chris Bowler and Leila Tirichine},
url = {https://doi.org/10.1038/s41598-021-82529-1},
doi = {10.1038/s41598-021-82529-1},
issn = {2045-2322},
year = {2021},
date = {2021-01-01},
journal = {Scientific Reports},
pages = {1--10},
publisher = {Nature Publishing Group UK},
abstract = {Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoguin, Antoine; Mohamed, Ouardia Ait; Bowler, Chris; Genovesio, Auguste; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum Article de journal
Dans: bioRxiv, 2021.
@article{Hoguin2021.06.11.447926,
title = {Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum},
author = {Antoine Hoguin and Ouardia Ait Mohamed and Chris Bowler and Auguste Genovesio and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2021/06/11/2021.06.11.447926},
doi = {10.1101/2021.06.11.447926},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the transcriptional control of mainly transposable elements in mammals, plants, and fungi. Eukaryotes encode a diverse set of DNA methyltransferases that were iteratively acquired and lost during evolution. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes that include the main phytoplankton classes such as diatoms and dinoflagellates. However, little is known about the diversity of DNA methyltransferases and their role in the deposition and maintenance of DNA methylation in microalgae. We performed a phylogenetic analysis of DNA methyltransferase families found in marine microeukaryotes and show that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes family revisiting previously established phylogenies. Furthermore, we reveal a novel group of DNMTs with three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrate that the loss of the DNMT5 gene correlates with a global depletion of DNA methylation and overexpression of transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a pioneering view of the structure and function of a DNMT family in the SAR supergroup.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Rastogi, Achal; Cabanillas, Anne Flore Deton; Mohamed, Ouardia Ait; Cantrel, Catherine; Lombard, Berangère; Murik, Omer; Genovesio, Auguste; Bowler, Chris; Bouyer, Daniel; Loew, Damarys; Lin, Xin; Veluchamy, Alaguraj; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum Article de journal
Dans: New Phytologist, p. nph.17129, 2021, ISSN: 0028-646X.
@article{Zhao2020b,
title = {Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum},
author = {Xue Zhao and Achal Rastogi and Anne Flore {Deton Cabanillas} and Ouardia {Ait Mohamed} and Catherine Cantrel and Berangère Lombard and Omer Murik and Auguste Genovesio and Chris Bowler and Daniel Bouyer and Damarys Loew and Xin Lin and Alaguraj Veluchamy and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17129},
doi = {10.1111/nph.17129},
issn = {0028-646X},
year = {2021},
date = {2021-01-01},
urldate = {2020-12-01},
journal = {New Phytologist},
pages = {nph.17129},
publisher = {Blackwell Publishing Ltd},
abstract = {In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Armbrecht, Linda; Eisenhofer, Raphael; Utge, José; Sibert, Elizabeth C; Rocha, Fabio; Ward, Ryan; Karlusich, Juan José Pierella; Tirichine, Leila; Norris, Richard; Summers, Mindi; Bowler, Chris
Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics Article de journal
Dans: ISME Communications, vol. 1, no. 1, p. 1–10, 2021.
@article{armbrecht2021paleo,
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics},
author = {Linda Armbrecht and Raphael Eisenhofer and José Utge and Elizabeth C Sibert and Fabio Rocha and Ryan Ward and Juan José Pierella Karlusich and Leila Tirichine and Richard Norris and Mindi Summers and Chris Bowler},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {ISME Communications},
volume = {1},
number = {1},
pages = {1--10},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
5 publications
Ait-Mohamed, Ouardia; Vanclová, Anna M G Novák; Joli, Nathalie; Liang, Yue; Zhao, Xue; Genovesio, Auguste; Tirichine, Leila; Bowler, Chris; Dorrell, Richard G
PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum Article de journal
Dans: Frontiers in Plant Science, vol. 11, 2020, ISSN: 1664462X.
@article{Ait-Mohamed2020,
title = {PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum},
author = {Ouardia Ait-Mohamed and Anna M G {Novák Vanclová} and Nathalie Joli and Yue Liang and Xue Zhao and Auguste Genovesio and Leila Tirichine and Chris Bowler and Richard G Dorrell},
url = {https://pubmed.ncbi.nlm.nih.gov/33178253/},
doi = {10.3389/fpls.2020.590949},
issn = {1664462X},
year = {2020},
date = {2020-10-01},
journal = {Frontiers in Plant Science},
volume = {11},
publisher = {Frontiers Media S.A.},
abstract = {Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leila
Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies Chapitre d'ouvrage
Dans: The molecular life of diatoms, Springer Nature Switzerland AG, 2020.
@inbook{cEQ5:ZHAO_TIRICHINE:2020,
title = {Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies},
author = {Xue Zhao and Antoine Hoguin and Timothée Chaumier and Leila Tirichine},
year = {2020},
date = {2020-04-01},
booktitle = {The molecular life of diatoms},
publisher = {Springer Nature Switzerland AG},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Sato, Shinya; Nanjappa, Deepak; Dorrell, Richard G; Vieira, Fabio Rocha Jimenez; Kazamia, Elena; Tirichine, Leila; Veluchamy, Alaguraj; Heilig, Roland; Aury, Jean Marc; Jaillon, Olivier; Wincker, Patrick; Fussy, Zoltan; Obornik, Miroslav; Muñoz-Gómez, Sergio A; Mann, David G; Bowler, Chris; Zingone, Adriana
Dans: Scientific Reports, vol. 10, no. 1, p. 1–12, 2020, ISSN: 20452322.
@article{Sato2020,
title = {Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal},
author = {Shinya Sato and Deepak Nanjappa and Richard G Dorrell and Fabio Rocha Jimenez Vieira and Elena Kazamia and Leila Tirichine and Alaguraj Veluchamy and Roland Heilig and Jean Marc Aury and Olivier Jaillon and Patrick Wincker and Zoltan Fussy and Miroslav Obornik and Sergio A Mu{ñ}oz-Gómez and David G Mann and Chris Bowler and Adriana Zingone},
doi = {10.1038/s41598-020-65941-x},
issn = {20452322},
year = {2020},
date = {2020-01-01},
journal = {Scientific Reports},
volume = {10},
number = {1},
pages = {1--12},
abstract = {Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fan, Xiao; Han, Wentao; Teng, Linhong; Jiang, Peng; Zhang, Xiaowen; Xu, Dong; Li, Chang; Pellegrini, Matteo; Wu, Chunhui; Wang, Yitao; Kaczurowski, Michelle Joyce Slade; Lin, Xin; Tirichine, Leila; Mock, Thomas; Ye, Naihao
Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants Article de journal
Dans: New Phytologist, vol. 225, no. 1, p. 234–249, 2020, ISSN: 14698137.
@article{Fan2020,
title = {Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants},
author = {Xiao Fan and Wentao Han and Linhong Teng and Peng Jiang and Xiaowen Zhang and Dong Xu and Chang Li and Matteo Pellegrini and Chunhui Wu and Yitao Wang and Michelle Joyce Slade Kaczurowski and Xin Lin and Leila Tirichine and Thomas Mock and Naihao Ye},
doi = {10.1111/nph.16125},
issn = {14698137},
year = {2020},
date = {2020-01-01},
journal = {New Phytologist},
volume = {225},
number = {1},
pages = {234--249},
abstract = {Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Cabanillas, Anne Flore Deton; Veluchamy, Alaguraj; Bowler, Chris; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae Article de journal
Dans: Frontiers in Marine Science, vol. 7, p. 189, 2020, ISSN: 2296-7745.
@article{10.3389/fmars.2020.00189,
title = {Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae},
author = {Xue Zhao and Anne Flore {Deton Cabanillas} and Alaguraj Veluchamy and Chris Bowler and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00189},
doi = {10.3389/fmars.2020.00189},
issn = {2296-7745},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in Marine Science},
volume = {7},
pages = {189},
abstract = {Polycomb (PcG) and Trithorax (TrxG) complexes are two evolutionarily conserved epigenetic regulatory components that act antagonistically to regulate the expression of genes involved in cell differentiation and development in multicellular organisms. The absence of PcG in both yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that polycomb proteins might have evolved together with the emergence of multicellular organisms. However, high throughput sequencing of several microalgal genomes and transcriptomes reveals an unprecedented abundance and diversity of genes encoding the components of these complexes. We report here the diversity of genes encoding PcG and TrxG proteins in microalgae from the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) and detected at broad scale in Tara Oceans genomics datasets using a highly sensitive method called eDAF (enhanced Domain Architecture Filtering). Further, we explored the correlation between environmental factors measured during the Tara Oceans expedition and transcript levels of PcG and TrxG components. PcG and TrxG are responsible for the deposition of a number of histone marks among which a TrxG associated mark, H3K4me3 which we profiled genome wide in the model diatom Phaeodactylum tricornutum to understand its role in microalgae and revisited the previously published histone code and co-occurrence with other histone marks including the antagonizing Polycomb deposited mark H3K27me3.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
4 publications
Murik, Omer; Tirichine, Leila; Prihoda, Judit; Thomas, Yann; Araújo, Wagner L; Allen, Andrew E; Fernie, Alisdair R; Bowler, Chris
Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom Article de journal
Dans: New Phytologist, vol. 221, no. 3, p. 1303–1316, 2019, ISSN: 14698137.
@article{Murik2019,
title = {Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom},
author = {Omer Murik and Leila Tirichine and Judit Prihoda and Yann Thomas and Wagner L Ara{ú}jo and Andrew E Allen and Alisdair R Fernie and Chris Bowler},
doi = {10.1111/nph.15479},
issn = {14698137},
year = {2019},
date = {2019-01-01},
journal = {New Phytologist},
volume = {221},
number = {3},
pages = {1303--1316},
abstract = {Diatom dominance in contemporary aquatic environments indicates that they have developed unique and effective mechanisms to cope with the rapid and considerable fluctuations that characterize these environments. In view of their evolutionary history from a secondary endosymbiosis, inter-organellar regulation of biochemical activities may be of particular relevance. Diatom mitochondrial alternative oxidase (AOX) is believed to play a significant role in supplying chloroplasts with ATP produced in the mitochondria. Using the model diatom Phaeodactylum tricornutum we generated AOX knockdown lines, and followed sensitivity to stressors, photosynthesis and transcriptome and metabolome profiles of wild-type and knockdown lines. We show here that expression of the AOX gene is upregulated by various stresses including H 2 O 2 , heat, high light illumination, and iron or nitrogen limitation. AOX knockdown results in hypersensitivity to stress. Knockdown lines also show significantly reduced photosynthetic rates and their chloroplasts are more oxidized. Comparisons of transcriptome and metabolome profiles suggest a strong impact of AOX activity on gene expression, which is carried through to the level of the metabolome. Our data provide evidence for the involvement of mitochondrial AOX in processes central to the cell biology of diatoms, revealing that cross-talk between mitochondria and chloroplasts is crucial for maintaining sensitivity to changing environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huang, Ruiping; Ding, Jiancheng; Gao, Kunshan; de Carvalho, Maria Helena; Tirichine, Leila; Bowler, Chris; Lin, Xin
A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum Article de journal
Dans: Frontiers in Microbiology, vol. 9, p. 3342, 2019, ISSN: 1664-302X.
@article{10.3389/fmicb.2018.03342,
title = {A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum},
author = {Ruiping Huang and Jiancheng Ding and Kunshan Gao and Maria Helena de Carvalho and Leila Tirichine and Chris Bowler and Xin Lin},
url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03342},
doi = {10.3389/fmicb.2018.03342},
issn = {1664-302X},
year = {2019},
date = {2019-01-01},
journal = {Frontiers in Microbiology},
volume = {9},
pages = {3342},
abstract = {Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shao, Zhanru; Thomas, Yann; Hembach, Lea; Xing, Xiaohui; Duan, Delin; Moerschbacher, Bruno M; Bulone, Vincent; Tirichine, Leila; Bowler, Chris
Dans: New Phytologist, vol. 221, no. 4, p. 1890–1905, 2019, ISSN: 14698137.
@article{Shao2019,
title = {Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms},
author = {Zhanru Shao and Yann Thomas and Lea Hembach and Xiaohui Xing and Delin Duan and Bruno M Moerschbacher and Vincent Bulone and Leila Tirichine and Chris Bowler},
doi = {10.1111/nph.15510},
issn = {14698137},
year = {2019},
date = {2019-01-01},
journal = {New Phytologist},
volume = {221},
number = {4},
pages = {1890--1905},
abstract = {Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc 5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Caputi, L; Carradec, Q; Eveillard, D; Kirilovsky, A; Pelletier, E; Karlusich, J J Pierella; Vieira, F Rocha Jimenez; Villar, E; Chaffron, S; Malviya, S; Scalco, E; Acinas, S G; Alberti, A; Aury, J -M; Benoiston, A -S; Bertrand, A; Biard, T; Bittner, L; Boccara, M; Brum, J R; Brunet, C; Busseni, G; Carratalà, A; Claustre, H; Coelho, L P; Colin, S; Daniello, S; Silva, C Da; Core, M Del; Doré, H; Gasparini, S; Kokoszka, F; Jamet, J -L; Lejeusne, C; Lepoivre, C; Lescot, M; Lima-Mendez, G; Lombard, F; Lukeš, J; Maillet, N; Madoui, M -A; Martinez, E; Mazzocchi, M G; Néou, M B; Paz-Yepes, J; Poulain, J; Ramondenc, S; Romagnan, J -B; Roux, S; Manta, D Salvagio; Sanges, R; Speich, S; Sprovieri, M; Sunagawa, S; Taillandier, V; Tanaka, A; Tirichine, Leila; Trottier, Camille; Uitz, J; Veluchamy, A; Veselá, J; Vincent, F; Yau, S; Kandels-Lewis, S; Searson, S; Dimier, C; Picheral, M; Bork, P; Boss, E; de Vargas, C; Follows, M J; Grimsley, N; Guidi, L; Hingamp, P; Karsenti, E; Sordino, P; Stemmann, L; Sullivan, M B; Tagliabue, A; Zingone, A; Garczarek, L; DÓrtenzio, F; Testor, P; Not, F; DÁlcalà, M R; Wincker, P; Bowler, C; Iudicone, D
Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Article de journal
Dans: Global Biogeochemical Cycles, vol. 33, no. 3, 2019, ISSN: 19449224.
@article{Caputi2019,
title = {Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems},
author = {L Caputi and Q Carradec and D Eveillard and A Kirilovsky and E Pelletier and J J Pierella Karlusich and F Rocha Jimenez Vieira and E Villar and S Chaffron and S Malviya and E Scalco and S G Acinas and A Alberti and J -M Aury and A -S Benoiston and A Bertrand and T Biard and L Bittner and M Boccara and J R Brum and C Brunet and G Busseni and A Carratalà and H Claustre and L P Coelho and S Colin and S Daniello and C Da Silva and M Del Core and H Doré and S Gasparini and F Kokoszka and J -L Jamet and C Lejeusne and C Lepoivre and M Lescot and G Lima-Mendez and F Lombard and J Lukeš and N Maillet and M -A Madoui and E Martinez and M G Mazzocchi and M B Néou and J Paz-Yepes and J Poulain and S Ramondenc and J -B Romagnan and S Roux and D Salvagio Manta and R Sanges and S Speich and M Sprovieri and S Sunagawa and V Taillandier and A Tanaka and Leila Tirichine and Camille Trottier and J Uitz and A Veluchamy and J Veselá and F Vincent and S Yau and S Kandels-Lewis and S Searson and C Dimier and M Picheral and P Bork and E Boss and C de Vargas and M J Follows and N Grimsley and L Guidi and P Hingamp and E Karsenti and P Sordino and L Stemmann and M B Sullivan and A Tagliabue and A Zingone and L Garczarek and F DÓrtenzio and P Testor and F Not and M R DÁlcalà and P Wincker and C Bowler and D Iudicone},
doi = {10.1029/2018GB006022},
issn = {19449224},
year = {2019},
date = {2019-01-01},
journal = {Global Biogeochemical Cycles},
volume = {33},
number = {3},
abstract = {Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2018
Nomaguchi, Tatsuhiro; Maeda, Yoshiaki; Yoshino, Tomoko; Asahi, Toru; Tirichine, Leila; Bowler, Chris; Tanaka, Tsuyoshi
Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris Article de journal
Dans: BMC Genomics, vol. 19, no. 1, 2018.
@article{avEQ5:Nomaguchi_TIRICHINE:2018,
title = {Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris},
author = {Tatsuhiro Nomaguchi and Yoshiaki Maeda and Tomoko Yoshino and Toru Asahi and Leila Tirichine and Chris Bowler and Tsuyoshi Tanaka},
url = {https://doi.org/10.1186%2Fs12864-018-4691-0},
doi = {10.1186/s12864-018-4691-0},
year = {2018},
date = {2018-05-01},
journal = {BMC Genomics},
volume = {19},
number = {1},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rastogi, Achal; Maheswari, Uma; Dorrell, Richard G; Vieira, Fabio Rocha Jimenez; Maumus, Florian; Kustka, Adam; McCarthy, James; Allen, Andy E; Kersey, Paul; Bowler, Chris; Tirichine, Leila
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum, genome and evolutionary origin of diatoms Article de journal
Dans: Scientific Reports, vol. 8, no. 1, 2018.
@article{avEQ5:Rastogi_TIRICHINE:2018,
title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum, genome and evolutionary origin of diatoms},
author = {Achal Rastogi and Uma Maheswari and Richard G Dorrell and Fabio Rocha Jimenez Vieira and Florian Maumus and Adam Kustka and James McCarthy and Andy E Allen and Paul Kersey and Chris Bowler and Leila Tirichine},
url = {https://doi.org/10.1038%2Fs41598-018-23106-x},
doi = {10.1038/s41598-018-23106-x},
year = {2018},
date = {2018-03-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Carradec, Quentin; Eric,; Pelletier,; Silva, Corinne Da; Alberti, Adriana; Seeleuthner, Yoann; Blanc-Mathieu, Romain; Lima-Mendez, Gipsi; Rocha, Fabio; Tirichine, Leila; Labadie, Karine; Kirilovsky, Amos; Bertrand, Alexis; Engelen, Stefan; Madoui, Mohammed-Amin; Méheust, Raphaël; Poulain, Julie; Romac, Sarah; Richter, Daniel J; Yoshikawa, Genki; Dimier, Céline; Kandels-Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Jaillon, Olivier; Aury, Jean-Marc; Karsenti, Eric; Sullivan, Matthew B; Sunagawa, Shinichi; Bork, Peer; Not, Fabrice; Hingamp, Pascal; Raes, Jeroen; Guidi, Lionel; Ogata, Hiroyuki; de Vargas, Colomban; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick
A global ocean atlas of eukaryotic genes Article de journal
Dans: Nature Communications, vol. 9, no. 1, 2018.
@article{avEQ5:Carradec_TIRICHINE:2018,
title = {A global ocean atlas of eukaryotic genes},
author = {Quentin Carradec and Eric and Pelletier and Corinne Da Silva and Adriana Alberti and Yoann Seeleuthner and Romain Blanc-Mathieu and Gipsi Lima-Mendez and Fabio Rocha and Leila Tirichine and Karine Labadie and Amos Kirilovsky and Alexis Bertrand and Stefan Engelen and Mohammed-Amin Madoui and Raphaël Méheust and Julie Poulain and Sarah Romac and Daniel J Richter and Genki Yoshikawa and Céline Dimier and Stefanie Kandels-Lewis and Marc Picheral and Sarah Searson and Olivier Jaillon and Jean-Marc Aury and Eric Karsenti and Matthew B Sullivan and Shinichi Sunagawa and Peer Bork and Fabrice Not and Pascal Hingamp and Jeroen Raes and Lionel Guidi and Hiroyuki Ogata and Colomban de Vargas and Daniele Iudicone and Chris Bowler and Patrick Wincker},
url = {https://doi.org/10.1038%2Fs41467-017-02342-1},
doi = {10.1038/s41467-017-02342-1},
year = {2018},
date = {2018-01-01},
journal = {Nature Communications},
volume = {9},
number = {1},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2017
Tirichine, Leila; Rastogi, Achal; Bowler, Chris
Recent progress in diatom genomics and epigenomics Article de journal
Dans: Current Opinion in Plant Biology, vol. 36, p. 46 - 55, 2017, ISSN: 1369-5266.
@article{avrEQ5:TIRICHINE:2017,
title = {Recent progress in diatom genomics and epigenomics},
author = {Leila Tirichine and Achal Rastogi and Chris Bowler},
url = {http://www.sciencedirect.com/science/article/pii/S1369526616301327},
doi = {10.1016/j.pbi.2017.02.001},
issn = {1369-5266},
year = {2017},
date = {2017-01-01},
journal = {Current Opinion in Plant Biology},
volume = {36},
pages = {46 - 55},
abstract = {Diatoms are one of the most diverse and successful groups of phytoplankton at the base of the food chain, sustaining life in the ocean and performing vital biogeochemical functions. The last fifteen years have witnessed the comprehensive analysis of several diatom genomes, revealing that they bear traces of their endosymbiotic origins from algal and heterotrophic ancestors, as well as significant gene transfer from bacteria. Their chimeric genomes are further regulated by a range of chromatin-based processes that are characteristic of both plant and animal genomes. We discuss the conservation of gene regulatory mechanisms in diatoms and propose that epigenetic processes may have a significant role in mediating responses to a highly dynamic and unpredictable environment in these organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2016
Rastogi, Achal; Murik, Omer; Bowler, Chris; Tirichine, Leila
PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing Article de journal
Dans: BMC Bioinformatics, vol. 17, no. 1, 2016.
@article{avEQ5:Rastogi_TIRICHINE:2016,
title = {PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing},
author = {Achal Rastogi and Omer Murik and Chris Bowler and Leila Tirichine},
url = {https://doi.org/10.1186%2Fs12859-016-1143-1},
doi = {10.1186/s12859-016-1143-1},
year = {2016},
date = {2016-07-01},
journal = {BMC Bioinformatics},
volume = {17},
number = {1},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; Thomas, Yann; Dingli, Florent; Rivarola, Maximo; Ott, Sandra; Liu, Xinyue; Sun, Yezhou; Rabinowicz, Pablo D; McCarthy, James; Allen, Andrew E; Loew, Damarys; Bowler, Chris; Tirichine, Leila
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum, Article de journal
Dans: Genome Biology, vol. 16, no. 1, 2015.
@article{avEQ5:Veluchamy_TIRICHINE:2015,
title = {An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum,},
author = {Alaguraj Veluchamy and Achal Rastogi and Xin Lin and Bérangère Lombard and Omer Murik and Yann Thomas and Florent Dingli and Maximo Rivarola and Sandra Ott and Xinyue Liu and Yezhou Sun and Pablo D Rabinowicz and James McCarthy and Andrew E Allen and Damarys Loew and Chris Bowler and Leila Tirichine},
url = {https://doi.org/10.1186%2Fs13059-015-0671-8},
doi = {10.1186/s13059-015-0671-8},
year = {2015},
date = {2015-05-01},
journal = {Genome Biology},
volume = {16},
number = {1},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morrissey, Joe; Sutak, Robert; Paz-Yepes, Javier; Tanaka, Atsuko; Moustafa, Ahmed; Veluchamy, Alaguraj; Thomas, Yann; Botebol, Hugo; Bouget, François-Yves; McQuaid, Jeffrey B.; Tirichine, Leila; Allen, Andrew E.; Lesuisse, Emmanuel; Bowler, Chris
A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake Article de journal
Dans: Current Biology, vol. 25, no. 3, p. 364–371, 2015.
@article{avEQ5:MORISSEY_TIRICHINE:2015,
title = {A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake},
author = {Joe Morrissey and Robert Sutak and Javier Paz-Yepes and Atsuko Tanaka and Ahmed Moustafa and Alaguraj Veluchamy and Yann Thomas and Hugo Botebol and François-Yves Bouget and Jeffrey~B. McQuaid and Leila Tirichine and Andrew~E. Allen and Emmanuel Lesuisse and Chris Bowler},
url = {https://doi.org/10.1016%2Fj.cub.2014.12.004},
doi = {10.1016/j.cub.2014.12.004},
year = {2015},
date = {2015-02-01},
journal = {Current Biology},
volume = {25},
number = {3},
pages = {364--371},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tanaka, Atsuko; Martino, Alessandra De; Amato, Alberto; Montsant, Anton; Mathieu, Benjamin; Rostaing, Philippe; Tirichine, Leila; Bowler, Chris
Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum, Article de journal
Dans: Protist, vol. 166, no. 5, p. 506 - 521, 2015, ISSN: 1434-4610.
@article{avEQ5:TANAKA_TIRICHINE:2015,
title = {Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum,},
author = {Atsuko Tanaka and Alessandra De Martino and Alberto Amato and Anton Montsant and Benjamin Mathieu and Philippe Rostaing and Leila Tirichine and Chris Bowler},
url = {http://www.sciencedirect.com/science/article/pii/S1434461015000498},
doi = {https://doi.org/10.1016/j.protis.2015.07.005},
issn = {1434-4610},
year = {2015},
date = {2015-01-01},
journal = {Protist},
volume = {166},
number = {5},
pages = {506 - 521},
abstract = {The marine pennate diatom Phaeodactylum tricornutum, has become a model for diatom biology, due to its ease of culture and accessibility to reverse genetics approaches. While several features underlying the molecular mechanisms of cell division have been described, morphological analyses are less advanced than they are in other diatoms. We therefore examined cell ultrastructure changes prior to and during cytokinesis. Following chloroplast division, cleavage furrows are formed at both longitudinal ends of the cell and are accompanied by significant vesicle transport. Although neither spindle nor microtubules were observed, the nucleus appeared to be split by the furrow after duplication of the Golgi apparatus. Finally, centripetal cytokinesis was completed by fusion of the furrows. Additionally, F-actin formed a ring structure and its diameter became smaller, accompanying the ingrowing furrows. To further analyse vesicular transport during cytokinesis, we generated transgenic cells expressing yellow fluorescent protein (YFP) fusions with putative diatom orthologs of small GTPase Sec4 and t-SNARE protein SyntaxinA. Time-lapse observations revealed that SyntaxinA-YFP localization expands from both cell tips toward the center, whereas Sec4-YFP was found in the Golgi and subsequently relocalizes to the future division plane. This work provides fundamental new information about cell replication processes in emphP. tricornutum,.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abida, Heni; Dolch, Lina-Juana; Meï, Coline; Villanova, Valeria; Conte, Melissa; Block, Maryse A; Finazzi, Giovanni; Bastien, Olivier; Tirichine, Leila; Bowler, Chris; Rébeillé, Fabrice; Petroutsos, Dimitris; Jouhet, Juliette; Maréchal, Eric
Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation in Phaeodactylum tricornutum, Article de journal
Dans: Plant Physiology, vol. 167, no. 1, p. 118–136, 2015, ISSN: 0032-0889.
@article{avEQ5:TIRICHINE:2015a,
title = {Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation in Phaeodactylum tricornutum,},
author = {Heni Abida and Lina-Juana Dolch and Coline Meï and Valeria Villanova and Melissa Conte and Maryse A Block and Giovanni Finazzi and Olivier Bastien and Leila Tirichine and Chris Bowler and Fabrice Rébeillé and Dimitris Petroutsos and Juliette Jouhet and Eric Maréchal},
url = {http://www.plantphysiol.org/content/167/1/118},
doi = {10.1104/pp.114.252395},
issn = {0032-0889},
year = {2015},
date = {2015-01-01},
journal = {Plant Physiology},
volume = {167},
number = {1},
pages = {118--136},
publisher = {American Society of Plant Biologists},
abstract = {Diatoms constitute a major phylum of phytoplankton biodiversity in ocean water and freshwater ecosystems. They are known to respond to some chemical variations of the environment by the accumulation of triacylglycerol, but the relative changes occurring in membrane glycerolipids have not yet been studied. Our goal was first to define a reference for the glycerolipidome of the marine model diatom Phaeodactylum tricornutum,, a necessary prerequisite to characterize and dissect the lipid metabolic routes that are orchestrated and regulated to build up each subcellular membrane compartment. By combining multiple analytical techniques, we determined the glycerolipid profile of emphP. tricornutum, grown with various levels of nitrogen or phosphorus supplies. In different emphP. tricornutum, accessions collected worldwide, a deprivation of either nutrient triggered an accumulation of triacylglycerol, but with different time scales and magnitudes. We investigated in depth the effect of nutrient starvation on the Pt1 strain (Culture Collection of Algae and Protozoa no. 1055/3). Nitrogen deprivation was the more severe stress, triggering thylakoid senescence and growth arrest. By contrast, phosphorus deprivation induced a stepwise adaptive response. The time scale of the glycerolipidome changes and the comparison with large-scale transcriptome studies were consistent with an exhaustion of unknown primary phosphorus-storage molecules (possibly polyphosphate) and a transcriptional control of some genes coding for specific lipid synthesis enzymes. We propose that phospholipids are secondary phosphorus-storage molecules broken down upon phosphorus deprivation, while nonphosphorus lipids are synthesized consistently with a phosphatidylglycerol-to-sulfolipid and a phosphatidycholine-to-betaine lipid replacement followed by a late accumulation of triacylglycerol.GlossaryNnitrogenPphosphorusPCphosphatidylcholinePGphosphatidylglycerolSQDGsulfoquinovosyldiacylglycerolBLbetaine lipidsMGDGmonogalactosyldiacylglycerolDGDGdigalactosyldiacylglycerolTAGtriacylglycerolDAGdiacylglycerolERendoplasmic reticulumPEphosphatidylethanolamineFv/Fmphotosynthetic capacityFAMEfatty acid methyl esterGC-FIDgas chromatography and flame ionization detectionFAfatty acidMSmass spectrometryDGTAdiacylglyceryl-hydroxymethyl-N,N,N-trimethyl-β-alanineDGTSdiacylglyceryl-N,N,N-trimethylhomoserinem/zmass-to-charge ratioMS2tandem mass spectrometryPIphosphatidylinositideCDP-DAGcytidine diphosphate-diacylglycerolESAWenriched seawater, artificial water},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stagiaires encadrés :
- Théo Ferré , Master microbiologie fondamentale et appliquée , Université de Bretagne occidentale (UBO, Brest)
- Chaima NACIRI , spécialisation Transition Environnementale et Durabilité, Ecole Supérieure d'Agriculture d'Angers
- Maina BON , Ingénieur Horticulture et Paysage, Institut Agro Rennes-Angers
- Clément POULAIN , Polytech Nantes, Nantes Université
- Clara GUILLOUCHE , Licence Sciences de la Vie parcours BCM option ABT, Nantes Université
- Nikunj SHARMA , doctorant en échange, Université du Québec à Trois-Rivières
- Irene ROMERO RODRIGUEZ , M1 Microbiologie Fondamentale et Appliquée, Université de Bretagne Occidentale