Les diatomees sont des algues brunes unicellulaires de la lignee stramenopile. Les diatomees sont... more Les diatomees sont des algues brunes unicellulaires de la lignee stramenopile. Les diatomees sont parmi les eucaryotes les plus divers et constituent un groupe majeur du phytoplancton. La methylation du carbone 5 de la cytosine est une marque epigenetique impliquee dans la repression des elements transposables, l'etablissement et le maintien de l'empreinte genomique et l'inactivation du chromosome X chez les mammiferes. Cette these fournit une description approfondie des machineries moleculaire de la methylation de l'ADN dans les differentes lignees de Stramenopile-Alevolates-Rhizaria. Nous demontrons egalement pour la premiere fois que l’enzyme DNMT5 est necessaire a la propagation des profils de methylation de l’ADN et a la repression des elements transposables dans la diatomee modele Phaeodactylum tricornutum. Les progres recents dans les technologies de sequencage a haut debit ont revele que les effets alleliques sont plus repandus qu'on ne le pensait auparav...
Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the tr... more 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 CRISP...
Recent advances in next generation sequencing technologies have allowed the discovery of widespre... more 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 c...
Les diatomees sont des algues brunes unicellulaires de la lignee stramenopile. Les diatomees sont... more Les diatomees sont des algues brunes unicellulaires de la lignee stramenopile. Les diatomees sont parmi les eucaryotes les plus divers et constituent un groupe majeur du phytoplancton. La methylation du carbone 5 de la cytosine est une marque epigenetique impliquee dans la repression des elements transposables, l'etablissement et le maintien de l'empreinte genomique et l'inactivation du chromosome X chez les mammiferes. Cette these fournit une description approfondie des machineries moleculaire de la methylation de l'ADN dans les differentes lignees de Stramenopile-Alevolates-Rhizaria. Nous demontrons egalement pour la premiere fois que l’enzyme DNMT5 est necessaire a la propagation des profils de methylation de l’ADN et a la repression des elements transposables dans la diatomee modele Phaeodactylum tricornutum. Les progres recents dans les technologies de sequencage a haut debit ont revele que les effets alleliques sont plus repandus qu'on ne le pensait auparav...
Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the tr... more 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 CRISP...
Recent advances in next generation sequencing technologies have allowed the discovery of widespre... more 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 c...
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Papers by Antoine Hoguin