@article{Wu2025,

title = {The RING1 subunit of Polycomb Repressive Complex 1 monoubiquitinates histone H2A                    and mediates repression independently of Polycomb Repressive Complex 2 in the model diatom                    \textit{Phaeodactylum tricornutum}},

author = {Yue Wu and Xue Zhao and Jing Xuan Chen and Timothée Chaumier and Leïla Tirichine},

doi = {10.1111/nph.70802},

issn = {1469-8137},

year  = {2026},

date = {2026-03-00},

urldate = {2026-03-00},

journal = {New Phytologist},

volume = {249},

number = {5},

pages = {2421--2434},

publisher = {Wiley},

abstract = {<jats:title>Summary</jats:title>

                  <jats:p>

                    <jats:list list-type="bullet">

                      <jats:list-item>

                        <jats:p>

                          Polycomb Repressive Complex 1 (PRC1) and its associated mark, H2A monoubiquitination (H2Aub), cooperate with PRC2 for transcriptional silencing in multicellular organisms. However, PRC1 is absent from many unicellular lineages, leaving its functional conservation and relationship with PRC2 unclear. In the model diatom

                          <jats:italic>Phaeodactylum tricornutum</jats:italic>

                          , the role of the PRC1 subunit RING1 was investigated to assess whether PRC1‐mediated repression is evolutionary conserved and how it interacts with PRC2.

                        </jats:p>

                      </jats:list-item>

                      <jats:list-item>

                        <jats:p>RING1 knockout mutants were generated to investigate H2Aub deposition. Genome‐wide H2Aub profiles were integrated with existing H3K27me3 maps, and transcriptome analyses were performed to compare RING1 and the PRC2 catalytic subunit Enhancer of Zeste mutants, thereby evaluating their respective contributions to gene and transposable elements (TEs) repression.</jats:p>

                      </jats:list-item>

                      <jats:list-item>

                        <jats:p>Loss of RING1 abolished H2Aub and revealed that H2Aub predominantly marks repressed genes lacking H3K27me3, while both marks colocalize on TEs. Transcriptome data indicate that H2Aub primarily mediates repression of genes with high H2Aub enrichment, whereas TEs marked by both H2Aub and H3K27me3 are mainly regulated by H3K27me3.</jats:p>

                      </jats:list-item>

                      <jats:list-item>

                        <jats:p>

                          These results demonstrate that PRC1 and PRC2, which originated before multicellularity, act independently to establish transcriptional silencing in

                          <jats:italic>P. tricornutum</jats:italic>

                          . PRC1 is functionally conserved in this diatom, with H2Aub and H3K27me3 fulfilling distinct yet complementary regulatory roles.

                        </jats:p>

                      </jats:list-item>

                    </jats:list>

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}