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Project I.) Chromatin mobility & DNA Repair


It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and rearrangement are involved in various biological processes, including gene regulation and the maintenance of genome stability. Maintaining DNA integrity is vital for the survival of all living organisms, and plant cells are constantly subjected to a variety of assaults that can compromise DNA stability. Despite this constant threat, plant cells maintain DNA structure remarkably well. However, little is known about how plants repair DNA in the context of chromatin spatial organization in the nucleus. This is a critical aspect since repair does not occur on isolated DNA strands but within the 3D structure of the cell nucleus. Our recent findings have shown that double-strand breaks (DSBs) increase chromatin mobility both locally (at sites of damage) and globally (genome-wide), yet the molecular mechanisms remain unknown. In this project, we are employing quantitative live fluorescence imaging, single-molecule RNA labeling methods, and molecular genetics to investigate the mechanisms that regulate mobility, identify new molecular factors involved in regulating chromatin dynamics, and evaluate the consequences of altered mobility on genome integrity.


Project II.) Nuclear Organization


Nuclear architecture is not only important for the efficient compaction and decompaction of the genome during cell division, but has important functions in coordinating gene regulatory networks and orchestrating cellular identity. Changes in nuclear organization are considered an important complement to epigenetic mechanisms contributing to robust and stable gene silencing. Recruitment of Polycomb Group (PcG) proteins to their target genes not only modulates local chromatin structure but also mediates distant interactions between regulatory sequences and shapes the global nuclear architecture, thereby regulation gene silencing at multiple scales. However, how the multiple layers of Polycomb regulation interconnect mechanistically to reinforce each other’s activity remains unclear. In our group we address the cause-consequence relationship Polycomb-mediated gene regulation and subnuclear chromatin organization?

Project III.) Transcription traffic control:


Gene transcription is fundamental to all life. The recent developments in genomics and bioinformatics have unveiled an unexpected complexity of the eukaryotic transcriptome. A surprise that emerged is the prevalence of transcription on antisense orientation of protein-coding genes. While the genome-wide role for antisense transcription is subject of obvious interest, its sheer existence can come at a cost for genome integrity. RNA Polymerases (RNAPII) transcribing opposite strands cannot bypass each other and head-to-head RNAPII collisions are likely to be harmful for the cells leading to gene blockage, backtracking or DNA damage. . In our group, we combine cell biology, molecular biology, biochemistry, mathematical modelling and single-molecule approaches to understand how transcription of sense/antisense gene pairs is coordinated at the single locus level to avoid transcriptional conflicts, such as RNA polymerase II head-to-head collisions.


Project IV.) Single-molecule RNA FISH


We are also interested in developing quantitative methods to investigate gene expression in a spatial context. In particular, we specialize in single-molecule RNA FISH detection protocols for plants.

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