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Illuminating chromatin compaction in live cells and fixed tissues using SiR-DNA fluorescence lifetime

View ORCID ProfileColin Hockings, View ORCID ProfileChetan Poudel, Kevin A. Feeney, View ORCID ProfileClara L. Novo, Mehdi S. Hamouda, View ORCID ProfileIoanna Mela, View ORCID ProfileDavid Fernandez-Antoran, View ORCID ProfilePedro P. Vallejo-Ramirez, View ORCID ProfilePeter J. Rugg-Gunn, View ORCID ProfileKevin Chalut, View ORCID ProfileClemens F. Kaminski, View ORCID ProfileGabriele Kaminski-Schierle
doi: https://doi.org/10.1101/2020.05.02.073536
Colin Hockings
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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Chetan Poudel
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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Kevin A. Feeney
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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Clara L. Novo
2Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
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Mehdi S. Hamouda
3Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
4Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
5National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, MA, USA
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Ioanna Mela
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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David Fernandez-Antoran
6Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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  • ORCID record for David Fernandez-Antoran
Pedro P. Vallejo-Ramirez
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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  • ORCID record for Pedro P. Vallejo-Ramirez
Peter J. Rugg-Gunn
2Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
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  • ORCID record for Peter J. Rugg-Gunn
Kevin Chalut
3Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
4Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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Clemens F. Kaminski
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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  • ORCID record for Clemens F. Kaminski
Gabriele Kaminski-Schierle
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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  • ORCID record for Gabriele Kaminski-Schierle
  • For correspondence: gsk20@cam.ac.uk
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Abstract

The global compaction state of chromatin in a nucleus is an important component of cell identity that has been difficult to measure. We have developed a quantitative method to measure the chromatin compaction state in both live and fixed cells, without the need for genetic modification, using the fluorescence lifetime of SiR-DNA dye. After optimising this method using live cancer cell lines treated to induce chromatin compaction or decompaction, we observed chromatin compaction in differentiating epithelial cells in fixed tissue sections, as well as local decompaction foci that may represent transcription factories. In addition, we shed new light on chromatin decompaction during embryonic stem cell transition out of their naïve pluripotent state. This method will be useful to studies of nuclear architecture, and may be easy, cheap, and accessible enough to serve as a general assay of ‘stem-ness’.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 02, 2020.
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Illuminating chromatin compaction in live cells and fixed tissues using SiR-DNA fluorescence lifetime
Colin Hockings, Chetan Poudel, Kevin A. Feeney, Clara L. Novo, Mehdi S. Hamouda, Ioanna Mela, David Fernandez-Antoran, Pedro P. Vallejo-Ramirez, Peter J. Rugg-Gunn, Kevin Chalut, Clemens F. Kaminski, Gabriele Kaminski-Schierle
bioRxiv 2020.05.02.073536; doi: https://doi.org/10.1101/2020.05.02.073536
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Illuminating chromatin compaction in live cells and fixed tissues using SiR-DNA fluorescence lifetime
Colin Hockings, Chetan Poudel, Kevin A. Feeney, Clara L. Novo, Mehdi S. Hamouda, Ioanna Mela, David Fernandez-Antoran, Pedro P. Vallejo-Ramirez, Peter J. Rugg-Gunn, Kevin Chalut, Clemens F. Kaminski, Gabriele Kaminski-Schierle
bioRxiv 2020.05.02.073536; doi: https://doi.org/10.1101/2020.05.02.073536

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