INDIVIDUAL RESEARCH PROJECT 9
Elucidating the role of cold-induced spatial clustering at the FLC locus during Polycomb-mediated gene silencing
Abstract
Investigate the functional connection between physical clustering and epigenetic silencing of the major flowering regulator FLOWERING LOCUS C (FLC) locus. Our previous findings revealed that cold-induced epigenetic silencing of FLC is accompanied by the physical clustering of FLC alleles7, suggesting a coordinated mechanism linking chromatin organization with gene expression regulation.
Here, we will: (Obj1) Investigate the relationship between clustering and transcriptional output by measuring FLC nascent transcript levels (using single molecule RNA FISH (smFISH)) in relation to FLC positioning (using DNA FISH) in fixed tissues, imaged in 3D at enhanced resolution (Airyscan). (Obj2) Elucidate the impact of clustering on chromatin mobility at the FLC locus tagged with the ANCHOR system2 and imaged in whole-mount roots using spinning disk imaging (S1) before and after silencing. (Obj3) Determine the impact of Polycomb– group (PRC2) related chromatin regulators required for FLC silencing on FLC clustering by analysing candidate mutants (vin3, vrn1, vrn5) using the same approach as in Obj1 and 2; (Obj4) Investigate the temporal dynamics of FLC mobility and heritability of FLC clustering through cell division during cold-mediated gene silencing using lightsheet imaging (S2) in live roots. Image analysis (registration, segmentation, tracking, quantification) will be done using ChromTrack3D tools.
More information
Training benefits
- Conceptual and practical training in epigenetics/chromatin regulation.
- Hands-on training in confocal microscopy, live-cell imaging, and single-molecule RNA imaging.
- Image analysis using modern AI-based tools for segmentation, tracking, and quantification.
- Structured teaching and mentoring experience with feedback on pedagogy and communication.
Requirements
Applicants must hold a Master’s degree, have basic molecular biology skills, and a strong interest in cell biology/microscopy. Proof of English proficiency (e.g., TOEFL/IELTS/Cambridge) is required.
Environment
The Department of Plant Biology at SLU Uppsala (Sweden) is part of Uppsala BioCenter, an interdisciplinary hub spanning plant biology, mycology, microbiology, computational genetics, and biotechnology. It offers modern growth facilities and bioimaging/molecular platforms, and is part of the Linnean Centre for Plant Biology, linking SLU and Uppsala University.
