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HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

Madeline M. Keenen, David Brown, Lucy D. Brennan, Roman Renger, Harrison Khoo, Christopher R. Carlson, Bo Huang, Stephan W. Grill, Geeta J. Narlikar, Sy Redding
doi: https://doi.org/10.1101/2020.10.30.362772
Madeline M. Keenen
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, USA
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David Brown
2Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA
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Lucy D. Brennan
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, USA
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Roman Renger
3Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden, Germany
4German Center for Neurodegenerative Diseases (DZNE), Germany
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Harrison Khoo
5Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Christopher R. Carlson
6Department of Physiology, University of California, San Francisco, San Francisco, California 94158, USA
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Bo Huang
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, USA
2Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA
7Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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Stephan W. Grill
3Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden, Germany
8Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
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Geeta J. Narlikar
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, USA
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  • For correspondence: geeta.narlikar@ucsf.edu
Sy Redding
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, USA
9Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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  • For correspondence: syeugene.redding@ucsf.edu
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Abstract

In mammals HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog’s DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.

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 4.0 International license.
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Posted October 31, 2020.
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HP1 proteins compact DNA into mechanically and positionally stable phase separated domains
Madeline M. Keenen, David Brown, Lucy D. Brennan, Roman Renger, Harrison Khoo, Christopher R. Carlson, Bo Huang, Stephan W. Grill, Geeta J. Narlikar, Sy Redding
bioRxiv 2020.10.30.362772; doi: https://doi.org/10.1101/2020.10.30.362772
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HP1 proteins compact DNA into mechanically and positionally stable phase separated domains
Madeline M. Keenen, David Brown, Lucy D. Brennan, Roman Renger, Harrison Khoo, Christopher R. Carlson, Bo Huang, Stephan W. Grill, Geeta J. Narlikar, Sy Redding
bioRxiv 2020.10.30.362772; doi: https://doi.org/10.1101/2020.10.30.362772

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