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.

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.

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?

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

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.

• 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.

The goal of of B4 is to characterize the diversity of condensates across animal species and to elucidate how these differences contribute to species-specific kinetics and developmental tempo.

Different animal species exhibit distinct biological tempos. For instance, human gestation takes about 9 months, whereas in mice it lasts only around 20 days. The Ebisuya group investigates these species-specific tempos using the “stem cell zoo,” a collection of mammalian stem cell lines, and has demonstrated that cellular environments differ across species. The Hyman group focuses on the physical properties of biomolecular condensates both in vitro and in cells. In collaboration, the groups recently found that the morphology of several condensates involved in gene expression processes differs between species. A key open question is whether such species-specific condensate properties influence biochemical reaction kinetics and thereby contribute to differences in biological tempo. Project B4 aims to address this fundamental question by systematically measuring the kinetics of condensates and associated cellular processes.

1. How do the kinetics and morphology of condensates vary across species?
2. What are the underlying mechanisms that give rise to these species-specific condensate properties?
3. Do such differential condensate properties contribute to species-specific cellular kinetics and biological tempo?

Quantitative characterization of condensates and gene expression kinetics across species

The student will receive training in cell and stem cell biology, advanced imaging and image analysis, as well as biophysical and biochemical approaches.

• Student candidates should hold a Master’s degree in biology, physics, or a related field. Candidates are expected to have hands-on experience with laboratory experiments; prior experience with cell cultures and/or imaging is a plus.

The goal of of B3 is to understand how condensate proteomes and their functions evolve. We aim to decipher which sequence perturbations can lead to gain/loss of condensates and tune specific molecular inter-actions within condensates in evolution and disease.

Extensive research on condensates focused on identifying their components, material proper-ties, and function. However, we still lack understanding of the mechanisms that target proteins into condensates and how condensates emerged during evolution. Building on the hypothesis that localization into condensates is encoded in protein sequences, we aim to advance the sequence-function mapping of condensate forming proteins and specifically intrinsically disordered regions (IDRs) that are common in condensates. Here, we will study not only genetic mutations but also phenotypic mutations that occur via transcription and translation errors, which we study in the Toth-Petroczy group. In collaboration with the Hyman group we built a condensate protein database that revealed wide-spread occurrence of condensates across the tree of life. Based on this curated data, we developed a machine learning algorithm to predict condensate proteins in any organism. Further, we have designed a suit of alignment-free algorithms to assess homology between unalignable IDR sequences (SHARK-dive) and developed a method to identify conserved motifs within a set of homologous IDR sequences (SHARK-capture). These tools allow us to address the origin and evolution of condensates and their proteomes, as well as to identify conserved and functional sequence features.

1. How do condensate proteomes change in evolution?
2. How do sequence perturbations impact condensate formation?

The evolution of condensate proteomes

The PhD students will be trained in data science, coding, machine learning, statistics, and image analysis, mass spectrometry, molecular biology, biochemistry and biophysics techniques in collaborations with experimental groups.

• Candidates have a Masters degree in biology, data science, or related fields
• Candidates should have a sound basis in computational or evolutionary biology, or closely related fields.
• Experience in coding and omics data analysis are expected