FRET-FISH offers new possibilities for understanding the mechanisms behind dysregulation of gene expression in disease

In a recent paper published in Nature Communications, Magda Bienkos' research group in KI's Department of Microbiology, Oncology and Cell Biology proposed a method
called FRET-FISH.
This method combines fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at selected loci in single cells
.

Nicolas Croceto is one of the main authors of the paper, and here is his interview
.

In this study, we describe a method – FRET-FISH – for measuring chromatin compaction (i.
e.
, the amount of DNA packed at a given volume) at a specific genomic location in a single cell, using a combination of two well-established microscopy methods: fluorescence in situ hybridization (FISH) and fluorescence resonance energy transfer (FRET).

Until now, chromatin compaction in specific genomic regions had not been possible to measure with a microscope, so our FRET-FISH method represents the first solution
to achieve this.

Why are these results important?

Chromatin compaction is essential for the regulation of gene expression, and the loss of proper gene regulation can lead to major diseases such as cancer
.
Therefore, having a tool for chromatin compaction that can be used to study genes involved in human diseases, such as cancer-associated genes, opens up new possibilities
for understanding the mechanisms by which gene expression disorders are altered in disease.

How can this new knowledge contribute to improving human health?

As mentioned earlier, our new method can be used to study how chromatin compaction changes
during carcinogenic processes, or in cancer cells exposed to drugs that alter chromatin compaction in the nucleus.
We also envision that one day, FRET-FISH may be used as an early diagnostic tool to detect changes in chromatin compaction in normal cells that are high-risk signals
for transformation into cancer cells.

How did you conduct this research?

The idea for FRET-FISH was originally conceived by Ana Mota, a PhD student in our research group, who was interested in
observing the fine structure of chromatin under light microscopy.
Despite the relative simplicity of the idea, Anna had to go through many cycles of trial and error until the method was robust enough to provide reproducible results
.
Once we were confident that FRET-FISH was indeed able to detect differences in chromatin compaction in a reproducible way, we started using it to explore chromatin compaction
in different situations.
For example, we used FRET-FISH to study how chromatin compaction for specific genes changes with cell proliferation, or when cells are exposed to drugs that alter chromatin compaction throughout the nucleus
.

Overall, it wasn't an easy journey, but it was certainly an enriching learning experience for everyone involved in the project

What's next for your research?

Our lab is primarily interested
in understanding how DNA folds in the nucleus and how the three-dimensional (3D) organization of the genome controls gene expression and influences the formation of potentially pathogenic mutations.
FRET-FISH is a powerful addition
to the toolbox we already have to study three-dimensional genomes in different cell and tissue types.
We anticipate that further development of this method will increase the number of DNA sites that can be visualized simultaneously, allowing us to measure chromatin compaction of multiple disease-related genes in the same cell
.
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