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Mota A, Berezicki S, Wernersson E, Harbers L, Li-Wang X, Gradin K, Peuckert C, Crosetto N, Bienko M. FRET-FISH probes chromatin compaction at individual genomic loci in single cells. Nat Commun 2022; 13:6680. [PMID: 36335096 PMCID: PMC9637210 DOI: 10.1038/s41467-022-34183-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
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.
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Affiliation(s)
- Ana Mota
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Szymon Berezicki
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Erik Wernersson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Xiaoze Li-Wang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Katarina Gradin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
| | - Christiane Peuckert
- Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm, Sweden
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
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