Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

Amy R. Strom; Yoonji Kim; Hongbo Zhao; Yi Che Chang; Natalia D. Orlovsky; Andrej Košmrlj; Cornelis Storm; Clifford P. Brangwynne

doi:10.1016/j.cell.2024.07.034

Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

Amy R. Strom
, Yoonji Kim
, Hongbo Zhao
, Yi Che Chang
, Natalia D. Orlovsky
, Andrej Košmrlj
, Cornelis Storm
, Clifford P. Brangwynne (Corresponding author)

Research output: Contribution to journal › Article › Academic › peer-review

54 Citations (Scopus)

435 Downloads (Pure)

Abstract

Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.

Original language	English
Article number	e20
Pages (from-to)	5282-5297
Number of pages	16
Journal	Cell
Volume	187
Issue number	19
DOIs	https://doi.org/10.1016/j.cell.2024.07.034
Publication status	Published - 19 Sept 2024

Funding

This work was supported by the Howard Hughes Medical Institute , the Princeton Biomolecular Condensate Program , the Princeton Center for Complex Materials , an MRSEC (NSF DMR-2011750 ), the St. Jude Collaborative on Membraneless Organelles , and the AFOSR MURI ( FA9550-20-1-0241 ). A.R.S. is a Life Science Research Foundation fellow through the Mark Foundation for Cancer Research (No. AWD1006303 ) and a K99/R00 Pathway to Independence Fellow ( K99CA276886-01 ). Y.K. was supported by the NSF GRFP ( DGE-2039656 ). H.Z. is supported by the Princeton Bioengineering Institute Innovators (PBI2) Postdoctoral Fellowship . We thank Leonid Mirny, Antoine Coulon, Simon Grosse-Holz, and Veer Keizer for helpful discussions regarding estimating pull force applied on chromatin loci and for sharing their \u201CRousepull\u201D code (https://github.com/OpenTrajectoryAnalysis/rousepull); Mikko Haataja for helpful advice on the modeling, Shunsuke Shimobayashi for the FUSN-miRFP670-TRF1 and HNRNPA1C-miRFP670-TRF1 constructs; Mackenzie Walls for the FUSN mutant original vectors; David Sanders for the FM5 vectors; Jing Xia for the array patterning protocol; Jessica Zhao for sharing code for MSD analysis; Lennard Wiesner for thoughtful comments on the manuscript; Evangelos Gatzogiannis for microscopy assistance; and other members of the Brangwynne Lab for helpful feedback and discussions. This work was supported by the Howard Hughes Medical Institute, the Princeton Biomolecular Condensate Program, the Princeton Center for Complex Materials, a MRSEC (NSF DMR-2011750), the St. Jude Collaborative on Membraneless Organelles, and the AFOSR MURI (FA9550-20-1-0241). A.R.S. is a Life Science Research Foundation fellow through the Mark Foundation for Cancer Research (No. AWD1006303) and a K99/R00 Pathway to Independence Fellow (K99CA276886-01). Y.K. was supported by the NSF GRFP (DGE-2039656). H.Z. is supported by the Princeton Bioengineering Institute Innovators (PBI2) Postdoctoral Fellowship. A.R.S. Y.K. and C.P.B. designed the study. A.R.S. and Y.K. performed experiments and analysis with advice from C.S. H.Z. and C.P.B. H.Z. created experiment-parallel simulations with advice from A.K. Y.-C.C. developed original technologies that provided the basis for these experiments, developed the dCas9-based VECTOR platform, and performed dCas9-based VECTOR experiments. N.D.O. performed telomere MSD tracking and pairwise data analysis. A.R.S. Y.K. and C.P.B. wrote the manuscript, and A.R.S. and Y.K. made the figures with contributions from all authors. C.P.B. is a scientific founder, Scientific Advisory Board member, shareholder, and consultant for Nereid Therapeutics.

Keywords

biomolecular condensates
capillary forces
nuclear mechanics
programmable genome organization
Viscosity
DNA/metabolism
Chromatin/metabolism
Humans
Elasticity
Biomolecular Condensates/metabolism
Genetic Loci

Access to Document

10.1016/j.cell.2024.07.034

pdfFinal published version, 9.92 MBLicence: CC BY

Cite this

@article{4de8d8510cd34949ab717e8c7b19bedb,

title = "Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity",

abstract = "Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.",

keywords = "biomolecular condensates, capillary forces, nuclear mechanics, programmable genome organization, Viscosity, DNA/metabolism, Chromatin/metabolism, Humans, Elasticity, Biomolecular Condensates/metabolism, Genetic Loci",

author = "Strom, \{Amy R.\} and Yoonji Kim and Hongbo Zhao and Chang, \{Yi Che\} and Orlovsky, \{Natalia D.\} and Andrej Ko{\v s}mrlj and Cornelis Storm and Brangwynne, \{Clifford P.\}",

year = "2024",

month = sep,

day = "19",

doi = "10.1016/j.cell.2024.07.034",

language = "English",

volume = "187",

pages = "5282--5297",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "19",

}

TY - JOUR

T1 - Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

AU - Strom, Amy R.

AU - Kim, Yoonji

AU - Zhao, Hongbo

AU - Chang, Yi Che

AU - Orlovsky, Natalia D.

AU - Košmrlj, Andrej

AU - Storm, Cornelis

AU - Brangwynne, Clifford P.

PY - 2024/9/19

Y1 - 2024/9/19

N2 - Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.

AB - Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.

KW - biomolecular condensates

KW - capillary forces

KW - nuclear mechanics

KW - programmable genome organization

KW - Viscosity

KW - DNA/metabolism

KW - Chromatin/metabolism

KW - Humans

KW - Elasticity

KW - Biomolecular Condensates/metabolism

KW - Genetic Loci

UR - https://www.scopus.com/pages/publications/85204745727

U2 - 10.1016/j.cell.2024.07.034

DO - 10.1016/j.cell.2024.07.034

M3 - Article

C2 - 39168125

AN - SCOPUS:85204745727

SN - 0092-8674

VL - 187

SP - 5282

EP - 5297

JO - Cell

JF - Cell

IS - 19

M1 - e20

ER -

Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this