Fluorescently labeled DNA and Microtubules

B5 - Role of condensates in epigenetics

Role of condensates in epigenetics (B5)

Objective

The goal of of B5 is to understand the physical mechanism behind the maintenance of the epigenetic state of chromatin through multiple cell generations. This is achieved by combining experiments and the-ory to study a well-defined setup which includes chromatin stretching, polymer-assisted conden-sation and enzymatic reactions.

Project Description

During the duplication of chromosomes, epigenetic information which resided in posttranslational modifications on histone proteins is equally distributed between the two daughter chromosomes. We proposed recently that the missing epigenetic tags can be reconstructed with the help of condensates that are formed from proteins such as HP1. Polymer-assisted condensates are formed around stretches of heterochromatin and serve as liquid reaction containers where enzymes (such as SUV39H1 methylase) add missing tags. The Schiessel group has used their expertise in computer simulations on small model chromosomes to demonstrate that polymer-assisted condensates are capable of maintaining the epigenetic state through 40 generations, thus reaching the Hayflick limit. The Brugués group uses their expertise in single molecule approaches and cell free extracts to test these ideas by using optical tweezers where a full chromosome and single DNA strands can be held in place and stretched in the cytoplasm from Xenopus egg extracts, a system in which replication can be induced. We will quantify the dynamics of the epigenetic state and test whether it can be maintained in the presence of HP1 and SUV39H1 through multiple cell generations. Simulations and theory will study how increasing tension breaks up HP1 droplets, transforming chromosomes into strings of micelles.

B5 - Polymer-assisted condensation serves as reaction vessels to reconstruct missing epigenetic markers

Research questions

  1. Can we visualize experimentally HP1 condensates forming along stretched chromosomes?
  2. What happens to the number and sizes of HP1 droplets as one increases the tension and how does it depend on the epigenetic sequence written along the string of nucleosomes?
  3. Can we demonstrate that condensate formation is maintained through several duplications in the presence of enzymatic reactions but suppressed otherwise? Does the disruption of an epigenetic condensate (for example by force) lead to the loss of epigenetic memory?

Thesis Project Topic

  • Topic 1 (Schiessel): Geometry and function of co-polymer-assisted micelles (Theory)
  • Topic 2 (Brugués): Emergent properties of chromatin (Experimental)

Training

The PhD students in the theory part of the project will be trained in mathematical-analytical methods, various simulation methods and numerical concepts. The PhD students in the experimental part will be trained in quantitative microscopy, optical tweezers, condensate quantification and manipulation, DNA biophysics.

Profile of Prospective Students

  • Candidates have a Masters degree in physics or related fields.
  • Candidates should have a sound basis in biophysics, computational biology, or closely related fields.
  • Experience in computer simulations is expected in Topic 1.
  • Experience with in vitro reconstitution systems is a plus in Topic 2.

Explore other RTG Thesis Projects

Collaborations within the RTG

Click on the different project numbers (e.g. A1) to find out more about the theme of their ongoing collaborations and explore the project details

Collaboration matrix of RTG 3120
A2 - Biomolecular condensate regulation (Harmon) A4 - Theory and simulation of polymer-assisted condensates (Sommer) B2 - Characterizing the role of RNP granules in ALS (Sterneckert) A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann) A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams) A5 - Capillary forces and the force response of condensates (Jahnel and Grill) B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf) B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy) B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman) B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

A2 - Biomolecular condensate regulation (Harmon)

Project A2 Collaborations

A4 - Theory and simulation of polymer-assisted condensates (Sommer)

Project A4 Collaborations

B2 - Characterizing the role of RNP granules in ALS (Sterneckert)

Project B2 Collaborations

A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann)

Project A1 Collaborations

A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams)

Project A3 Collaborations

A5 - Capillary forces and the force response of condensates (Jahnel and Grill)

Project A5 Collaborations

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf)

Project B1 Collaborations

B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy)

Project B3 Collaborations

B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman)

Project B4 Collaborations

B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

Project B5 Collaborations

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation

Elucidating the mechanisms underlying mRNA translation regulation by condensation (B1)

Objective

The goal of of B1 is to characterize the molecular interaction landscape of immobile and mobile (translationally silenced and competent) nature of RNA molecules inside RNP granules to provide a mechanistic understanding of regulation in condensates and disease phenotypes

Project Description

RNP granules, such as neuronal transport granules (NTGs) or stress-induced RNP granules (SGs), are condensates that play key roles in translation regulation. Their aberrant state is as-sociated with neurodegeneration and cancer. RNP granule assembly and the underlying regula-tory mechanisms are not understood. Our preliminary data show that the RNA-binding protein Ras GTPase-activating protein-binding protein 1 (G3BP1) interacts with unfolded RNA molecules to assemble RNP granules. RNA accumulation in granules leads to RNA-RNA interactions, inhibiting RNA mobility and translatability. The DEAD-box RNA helicase (DDX3X) localizes to RNP granules to attenuate RNA-RNA interactions, rendering the condensates dynamic and ena-bling mRNA translation. DDX3X disease variants cannot resolve RNA-RNA interactions causing RNA granule persistence. We suggest that RNP granules mediate inhibitory RNA-RNA interactions, which must be modulated by RNA helicases to regulate RNA availability and translatability.

B1 - helicase DDX3X remodels RNA-RNA interactions inside reconstituted RNP granules

Research questions

  1. How do RNP granules regulate RNA availability and translatability in physiology and disease?
  2. How do RNA helicases regulate RNA structure, dynamics, and organization within RNP granules?

Thesis Project Topic

Topic 1: RNA structures and dynamics in multi-component biomolecular condensates (Schlierf)
Topic 2: Revealing the functional role of RNA-protein condensates in regulating RNA availability (Alberti)

Training

The PhD students will be trained in smFRET and FCS and analysis, advanced imaging and analysis, protein biochemistry and RNP-like granule reconstitution.

Profile of Prospective Students

  • Candidates have a Masters degree in physics, biology or related fields
  • Candidates should have a sound basis in biochemistry, biophysics, enzymology, quantitative biology, or closely related fields.
  • Experience in microscopy, in vitro reconstitution, and protein isolation methods are expected

Explore other RTG Thesis Projects

Collaborations within the RTG

Click on the different project numbers (e.g. A1) to find out more about the theme of their ongoing collaborations and explore the project details

Collaboration matrix of RTG 3120
A2 - Biomolecular condensate regulation (Harmon) A4 - Theory and simulation of polymer-assisted condensates (Sommer) B2 - Characterizing the role of RNP granules in ALS (Sterneckert) A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann) A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams) A5 - Capillary forces and the force response of condensates (Jahnel and Grill) B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf) B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy) B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman) B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

A2 - Biomolecular condensate regulation (Harmon)

Project A2 Collaborations

A4 - Theory and simulation of polymer-assisted condensates (Sommer)

Project A4 Collaborations

B2 - Characterizing the role of RNP granules in ALS (Sterneckert)

Project B2 Collaborations

A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann)

Project A1 Collaborations

A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams)

Project A3 Collaborations

A5 - Capillary forces and the force response of condensates (Jahnel and Grill)

Project A5 Collaborations

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf)

Project B1 Collaborations

B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy)

Project B3 Collaborations

B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman)

Project B4 Collaborations

B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

Project B5 Collaborations

Project A5 Thumbnail

A5 - Capillary forces and the force response of condensates

Capillary forces and the force response of condensates (A5)

Objective

The goal of of A5 is to understand how condensates respond to mechanical forces and how condensate-mediated capillary forces influence the shape and organization of biopolymers.

Project Description

Biomolecular condensates are mostly considered as special biochemical environments. However, due to their tendency to minimize their interfacial area, condensates generate relevant capillary forces that can bundle and bend soft cellular structures. Recently, the Grill lab has explored the mechanical effects of condensates on various biopolymers such as nucleic acids and cytoskeletal filaments. In collaboration with the Hyman and Jülicher groups, the Grill group has discovered the prewetting and co-condensation of transcription factors on DNA and that condensates can bundle DNA. Furthermore, the Grill group has discovered a condensate dynamic instability that is crucial to establishing the actin cell cortex during early nematode development. Finally, preliminary data from the Grill lab demonstrate shape changes of cortical condensates are likely driven by condensate surface tension and identify a mechanical role of DNA-binding proteins during the assembly of the nuclear periphery (Collaboration with von Appen group at MPI-CBG). Despite this progress, the rich interplay between condensate interfacial energies, condensate-polymer interaction energies, and biopolymer bending energies has not been systematically studied and remains poorly understood.

Research questions

1) How do condensates respond to mechanical forces and exert capillary forces on various cellular structures?

2) Can we predict the mechanical condensate-polymer behavior?

3) How to measure the interfacial properties and interaction energies of condensates and their substrates?

Thesis Project Topic

Regulatory RNA folding in and around condensates

Training

The PhD students will be trained in in soft matter physics concepts, single-molecule experiments, protein and nucleic acid molecular biology methods, data and image analysis methods and state-of-the-art instrumentation such as optical tweezers and light-sheet microscopy.

Profile of Prospective Students

  • Candidates have a Masters degree in physics, biology or related fields
  • Candidates should have a sound basis in (theoretical) biophysics, polymer science, quantitative biology, or closely related fields.
  • Experience in microscopy and protein isolation methods are expected

Explore other RTG Thesis Projects

Collaborations within the RTG

Click on the different project numbers (e.g. A1) to find out more about the theme of their ongoing collaborations and explore the project details

Collaboration matrix of RTG 3120
A2 - Biomolecular condensate regulation (Harmon) A4 - Theory and simulation of polymer-assisted condensates (Sommer) B2 - Characterizing the role of RNP granules in ALS (Sterneckert) A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann) A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams) A5 - Capillary forces and the force response of condensates (Jahnel and Grill) B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf) B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy) B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman) B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

A2 - Biomolecular condensate regulation (Harmon)

Project A2 Collaborations

A4 - Theory and simulation of polymer-assisted condensates (Sommer)

Project A4 Collaborations

B2 - Characterizing the role of RNP granules in ALS (Sterneckert)

Project B2 Collaborations

A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann)

Project A1 Collaborations

A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams)

Project A3 Collaborations

A5 - Capillary forces and the force response of condensates (Jahnel and Grill)

Project A5 Collaborations

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf)

Project B1 Collaborations

B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy)

Project B3 Collaborations

B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman)

Project B4 Collaborations

B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

Project B5 Collaborations

Project A1 Thumbnail

A1 - Role of surface condensation for the assembly of cortical proteins

Role of surface condensation for the assembly of cortical proteins (A1)

Objective

The goal of A1 is to understand how surface condensation of scaffold proteins at biological membranes can control the patterning and the mechanics of an acto-myosin cell cortex.

Research Description

The formation of epithelial tissue requires precise spatiotemporal control of cell surface properties such as formation of adhesion complexes that are linked to the cell cortex at the level of the cell membrane1,2. The Honigmann group has discovered that surface condensation of ZO scaffold proteins at the membrane is a mechanism that cells exploit to pattern adhesion complexes and the actin cortex3. In vitro reconstitutions have shown that ZO surface condensates can nucleate and bundle actin fibers, which can drive the formation of a variety of cortical patterns4-6. How ZO surface condensation and actin polymerization are linked and what mechanical properties emerge from this is not understood.

Research questions

How does surface condensation of ZO proteins induce actin recruitment and polymerization? and What are the mechanical properties of a condensed ZO1-actin cortex on the membrane?

Thesis Project Topic

Linking surface condensation of scaffold proteins to the assembly of cell junctions

Training

The PhD students will be trained in protein and membrane biochemistry methods including membrane reconstitutions, biophysical methods such as fluorescence fluctuation spectroscopy, in addition to super-resolution microscopy and image analysis methods.

Profile of Prospective Students

  • Candidates have a Masters degree in biophysics or related fields
  • Candidates are expected to have a solid basis in physics, biology, or related fields.
  • Experience in fluorescence microscopy is plus

References

  1. Roignot J, Peng X, Mostov K. Polarity in Mammalian Epithelial Morphogenesis. Cold Spring Harb Perspect Biol. 2013;5(2):a013789-a013789. https://doi.org/10.1101/cshperspect.a013789
  2. Mukenhirn M, Wang CH, Guyomar T, Bovyn MJ, Staddon MF, van der Veen RE, Maraspini R, Lu L, Martin-Lemaitre C, Sano M, Lehmann M, Hiraiwa T, Riveline D, Honigmann A. Tight junctions control lumen morphology via hydrostatic pressure and junctional tension. Dev Cell. https://doi.org/10.1016/j.devcel.2024.07.016
  3. Beutel O, Maraspini R, Pombo-García K, Martin-Lemaitre C, Honigmann A. Phase Separation of Zonula Occludens Proteins Drives Formation of Tight Junctions. Cell. 2019;179(4):923-936.e11. https://doi.org/10.1016/j.cell.2019.10.011
  4. Zhao X, Bartolucci G, Honigmann A, Jülicher F, Weber CA. Thermodynamics of wetting, prewetting and surface phase transitions with surface binding. New J Phys. 2021;23(12):123003. https://doi.org/10.1088/1367-2630/ac320b
  5. Pombo-García, K, Adame-Arana, O, Martin-Lemaitre, C, Jülicher, F, Honigmann, A. Membrane prewetting by condensates promotes tight junction belt formation. Nature. 2024; 632, 647–655. https://doi.org/10.1038/s41586-024-07726-0
  6. Sun, D, Zhao, X, Wiegand, T, Bartolucci, G, Martin-Lemaitre, C, Grill, S, Hyman, AA, Weber, C, Honigmann, A. Assembly of tight junction belts by surface condensation and actin elongation. bioRxiv. Published online 2023. https://doi.org/10.1101/2023.06.24.546380

Explore other RTG Thesis Projects

Collaborations within the RTG

Click on the different project numbers (e.g. A1) to find out more about the theme of their ongoing collaborations and explore the project details

Collaboration matrix of RTG 3120
A2 - Biomolecular condensate regulation (Harmon) A4 - Theory and simulation of polymer-assisted condensates (Sommer) B2 - Characterizing the role of RNP granules in ALS (Sterneckert) A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann) A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams) A5 - Capillary forces and the force response of condensates (Jahnel and Grill) B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf) B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy) B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman) B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

A2 - Biomolecular condensate regulation (Harmon)

Project A2 Collaborations

A4 - Theory and simulation of polymer-assisted condensates (Sommer)

Project A4 Collaborations

B2 - Characterizing the role of RNP granules in ALS (Sterneckert)

Project B2 Collaborations

A1 - Role of surface condensation for the assembly of cortical proteins (Honigmann)

Project A1 Collaborations

A3 - Spectroscopy and local interactions in condensates and organization of the cytoplasm (Adams)

Project A3 Collaborations

A5 - Capillary forces and the force response of condensates (Jahnel and Grill)

Project A5 Collaborations

B1 - Elucidating the mechanisms underlying mRNA translation regulation by condensation (biophysics and biochemistry) (Alberti and Schlierf)

Project B1 Collaborations

B3 - Sequence to function mapping of condensate proteomes (Toth-Petroczy)

Project B3 Collaborations

B4 - Role of condensates in biological time across mammals (Ebisuya and Hyman)

Project B4 Collaborations

B5 - Role of condensates in epigenetics (experiments and theory) (Brugués and Schiessel)

Project B5 Collaborations

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