PMID- 36335096
OWN - NLM
STAT- MEDLINE
DCOM- 20221108
LR  - 20221224
IS  - 2041-1723 (Electronic)
IS  - 2041-1723 (Linking)
VI  - 13
IP  - 1
DP  - 2022 Nov 5
TI  - FRET-FISH probes chromatin compaction at individual genomic loci in single cells.
PG  - 6680
LID - 10.1038/s41467-022-34183-y [doi]
LID - 6680
AB  - 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.
CI  - (c) 2022. The Author(s).
FAU - Mota, Ana
AU  - Mota A
AUID- ORCID: 0000-0001-8592-9764
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Berezicki, Szymon
AU  - Berezicki S
AUID- ORCID: 0000-0003-3980-6290
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Wernersson, Erik
AU  - Wernersson E
AUID- ORCID: 0000-0003-4778-1660
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Harbers, Luuk
AU  - Harbers L
AUID- ORCID: 0000-0003-3910-6497
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Li-Wang, Xiaoze
AU  - Li-Wang X
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Gradin, Katarina
AU  - Gradin K
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
FAU - Peuckert, Christiane
AU  - Peuckert C
AD  - Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren 
      Institute, Stockholm, Sweden.
FAU - Crosetto, Nicola
AU  - Crosetto N
AUID- ORCID: 0000-0002-3019-6978
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden.
AD  - Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
FAU - Bienko, Magda
AU  - Bienko M
AUID- ORCID: 0000-0002-6499-9082
AD  - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 
      Stockholm, SE-17165, Sweden. magda.bienko@ki.se.
AD  - Science for Life Laboratory, Tomtebodavagen 23A, Solna, SE-17165, Sweden. 
      magda.bienko@ki.se.
AD  - Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy. 
      magda.bienko@ki.se.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20221105
PL  - England
TA  - Nat Commun
JT  - Nature communications
JID - 101528555
RN  - 0 (Chromatin)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - *Chromatin/genetics
MH  - *Fluorescence Resonance Energy Transfer/methods
MH  - In Situ Hybridization, Fluorescence/methods
MH  - DNA/metabolism
MH  - Genomics
PMC - PMC9637210
COIS- The authors declare no competing interests.
EDAT- 2022/11/06 06:00
MHDA- 2022/11/09 06:00
PMCR- 2022/11/05
CRDT- 2022/11/06 00:14
PHST- 2021/12/01 00:00 [received]
PHST- 2022/10/14 00:00 [accepted]
PHST- 2022/11/06 00:14 [entrez]
PHST- 2022/11/06 06:00 [pubmed]
PHST- 2022/11/09 06:00 [medline]
PHST- 2022/11/05 00:00 [pmc-release]
AID - 10.1038/s41467-022-34183-y [pii]
AID - 34183 [pii]
AID - 10.1038/s41467-022-34183-y [doi]
PST - epublish
SO  - Nat Commun. 2022 Nov 5;13(1):6680. doi: 10.1038/s41467-022-34183-y.