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Project title:

The Polycomb Gatekeeper: PRC2-Mediated Genome Defence and Allele-Specific Expression in the Polar Diatom Fragilariopsis cylindrus

Highlights:

Overview:

The polar diatom Fragilariopsis cylindrus (Fig 1) is a key primary producer in Polar Oceans and a model for studying microbial adaptation to extreme polar environments. Its genome features unusual architecture, including extensive transposable element (TE) content and nearly 25% highly divergent alleles that exhibit differential expression in response to environmental changes (Mock et al., 2017; Paajanen et al., 2017). These genomic traits likely contribute to its phenotypic plasticity, though chromatin-based regulatory mechanisms remain unclear.

Polycomb Repressive Complex 2 (PRC2) deposits the repressive histone mark H3K27me3 and silences TEs across diverse eukaryotes, suggesting an ancient, conserved genome defence function (Hisanaga et al., 2023; Velanis et al., 2020). PRC2 also regulates allele-specific gene expression in plants, including allele-biased repression of imprinted genes in Arabidopsis thaliana (Zhang et al., 2018), indicating its potential role in controlling divergent allele activity.

This project hypothesizes that PRC2 acts as an ancestral genome defence pathway in F. cylindrus by repressing TEs and regulating environmentally responsive divergent alleles, linking genome stability with adaptive transcriptional plasticity. The study will first map H3K27me3 distribution under climate-relevant stressors—ocean warming and acidification—to assess whether Polycomb targets TEs, divergent alleles, or conventional genes preferentially. Chromatin profiles will then be integrated with strand-specific RNA sequencing to examine whether allele-specific expression changes correlate with differential H3K27me3 marking.

Functional significance of PRC2 will be tested via chemical perturbation, evaluating effects on TE expression, allele-specific transcription, cellular fitness, and stress responses. An optional extension will investigate interactions between DNA methylation and Polycomb repression at selected loci.

By combining environmental biology, epigenomics, and functional genomics, this project aims to elucidate chromatin-based regulation’s role in genome stability, transcriptional plasticity, and environmental adaptation in a crucial polar phytoplankton species. The findings will enhance understanding of molecular mechanisms underpinning resilience to climate-driven changes in polar marine ecosystems.

 

Methods:

Cultures of Fragilariopsis cylindrus will be exposed to climate-relevant stressors, including ocean warming and acidification. Core PRC2 components will be identified and characterised bioinformatically using available genome and transcriptome data. The genome-wide distribution of the repressive histone mark H3K27me3 will be mapped using low-input chromatin profiling methods, complemented by targeted ChIP-qPCR validation at selected transposable element (TE)-rich and highly divergent allelic loci.

Strand-specific RNA sequencing will quantify gene expression and allele-specific transcription under these environmental conditions. Integration of chromatin and transcriptomic datasets will assess whether differential H3K27me3 occupancy correlates with environmentally responsive allele-specific expression.

Functional roles of PRC2 will be evaluated through chemical inhibition, measuring effects on TE expression, allele-specific transcription, cellular growth and stress tolerance. Where appropriate, targeted DNA methylation analyses will investigate interactions between DNA methylation and Polycomb-mediated repression at candidate loci.

 

Training:

This project will provide training in environmental microbiology, algal culturing and physiology, wet lab molecular biology and epigenetics, epigenomics, transcriptomics, bioinformatics and data analysis. The student will gain hands-on experience in phytoplankton culturing, climate-stress experimentation, chromatin profiling, RNA sequencing and genome-scale data integration. Training will also be provided in statistical analysis, reproducible computational workflows, scientific writing, presentation skills, research ethics and open science practices. Together with CENTA training events, conferences and professional development opportunities, these activities will equip the student with a broad range of technical and transferable skills relevant to careers in academia, environmental research and the biotechnology sector.

 

Supervisors:

PI: Dr Christos Velanis christos.velanis@open.ac.uk -The Open University

Co-I: Dr Adam Woodhouse adam.woodhouse@open.ac.uk The Open University

Co-I: Prof. Thomas Mock T.Mock@uea.ac.uk – University of East Anglia