FRET-FISH probes chromatin compaction at individual genomic loci in single cells

Ana Mota, Szymon Berezicki, Erik Wernersson, Luuk Harbers, Xiaoze Li-Wang, Katarina Gradin, Christiane Peuckert, Nicola Crosetto and Magda Bienko ()
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Ana Mota: Tumor and Cell Biology, Karolinska Institutet
Szymon Berezicki: Tumor and Cell Biology, Karolinska Institutet
Erik Wernersson: Tumor and Cell Biology, Karolinska Institutet
Luuk Harbers: Tumor and Cell Biology, Karolinska Institutet
Xiaoze Li-Wang: Tumor and Cell Biology, Karolinska Institutet
Katarina Gradin: Tumor and Cell Biology, Karolinska Institutet
Christiane Peuckert: Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren Institute
Nicola Crosetto: Tumor and Cell Biology, Karolinska Institutet
Magda Bienko: Tumor and Cell Biology, Karolinska Institutet

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.

Date: 2022
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DOI: 10.1038/s41467-022-34183-y

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