Physics of liquid-drop compartment interaction in gene function
Lead Research Organisation:
University of Cambridge
Department Name: Physics
Abstract
Genome sequencing has advanced to the point that it can now be used as a routine tool. The challenge has moved to interpreting our genome - finding out how it functions. To answer this, knowledge of the linear sequences of DNA bases is not enough: after all, the different cells in our body (e.g. skin, heart, liver) contain the same DNA information. In contrast, genomes have intricate 3D spatial organizations that are sensitive to the biological context and are intimately linked to function. Not surprisingly, one of the big open challenges to understand gene behaviour is deciphering how the genome is organized in space and how this organization influences its function.
Inside mammalian cells, the genome is found in the form of chromatin - a polymer made of building blocks called nucleosomes. Our understanding of chromatin organization inside the cell nucleus is currently limited by the lack of 'close up views' and molecular-level mechanistic information of how nucleosome interactions are regulated by many highly coupled factors. Last year, breakthrough experiments (Gibson et al., 2019, Cell 179, 470-484), discovered a crucial, yet unexplored, parameter affecting chromatin structure: a system made of many short chromatin polymers has the fundamental ability to undergo liquid-liquid phase separation and form membraneless compartments. My aim is to develop a minimal coarse-grained model of chromatin to elucidate how changes in intrinsic properties of chromatin (e.g. linker DNA length, nucleosome DNA unwrapping, heterogeneity) module its ability to form phase-separated liquid droplets. Key open questions that my project will address are: What is the behaviour of nucleosomes inside phase separated domains? Can we explain the emergence of different phase-separated chromatin domains from changes in the intrinsic properties of chromatin? Can we predict the mesoscale physical properties of phase-separated chromatin domains from the differential behaviour of nucleosomes? How does differential nucleosome behaviour among phase-separated domains impact the interaction and coalescence of distinct domains?
This research will be achieved through the following specific objectives and novel methodology:
O1. To develop a novel low-resolution coarse-grained model of chromatin to investigate its liquid-liquid phase separating ability. This model will have a resolution of one bead per nucleosome and will be anchored
to the high-resolution chemically-accurate chromatin model of the Collepardo group (1 bead per amino acid and DNA basepair) and validated against published experimental data (Gibson et al., 2019, Cell 179, 470- 484), to incorporate a crucial, yet unaccounted for, feature: spontaneous DNA nucleosome unwrapping.
O2. To apply the model to investigate changes in chromatin liquid-liquid phase separation by modulation of intrinsic properties. I will apply the model described above to compute the full phase diagrams of chromatin via the Direct Coexistence Simulation method. This will allow me to investigate how changes in linker DNA length, ionic environment, and nucleosome DNA unwrapping influences the critical temperature for phase separation.
O3. To extend the model to account for binding of phase-separating architectural proteins and use it to understand nucleosome organization inside functional chromatin domains. This will allow me to understand how binding of architectural proteins coupled to intrinsic characteristics in chromatin structure influence the phase behaviour of chromatin. We will aim to compare our results using proteins that are correlated with the formation of active, inactive, and repressed domains in mammalian genomes. The understanding gained will be central to propose molecular mechanisms that explain the regulation of nucleosome organization inside structurally different chromatin phase-separated domains.
Inside mammalian cells, the genome is found in the form of chromatin - a polymer made of building blocks called nucleosomes. Our understanding of chromatin organization inside the cell nucleus is currently limited by the lack of 'close up views' and molecular-level mechanistic information of how nucleosome interactions are regulated by many highly coupled factors. Last year, breakthrough experiments (Gibson et al., 2019, Cell 179, 470-484), discovered a crucial, yet unexplored, parameter affecting chromatin structure: a system made of many short chromatin polymers has the fundamental ability to undergo liquid-liquid phase separation and form membraneless compartments. My aim is to develop a minimal coarse-grained model of chromatin to elucidate how changes in intrinsic properties of chromatin (e.g. linker DNA length, nucleosome DNA unwrapping, heterogeneity) module its ability to form phase-separated liquid droplets. Key open questions that my project will address are: What is the behaviour of nucleosomes inside phase separated domains? Can we explain the emergence of different phase-separated chromatin domains from changes in the intrinsic properties of chromatin? Can we predict the mesoscale physical properties of phase-separated chromatin domains from the differential behaviour of nucleosomes? How does differential nucleosome behaviour among phase-separated domains impact the interaction and coalescence of distinct domains?
This research will be achieved through the following specific objectives and novel methodology:
O1. To develop a novel low-resolution coarse-grained model of chromatin to investigate its liquid-liquid phase separating ability. This model will have a resolution of one bead per nucleosome and will be anchored
to the high-resolution chemically-accurate chromatin model of the Collepardo group (1 bead per amino acid and DNA basepair) and validated against published experimental data (Gibson et al., 2019, Cell 179, 470- 484), to incorporate a crucial, yet unaccounted for, feature: spontaneous DNA nucleosome unwrapping.
O2. To apply the model to investigate changes in chromatin liquid-liquid phase separation by modulation of intrinsic properties. I will apply the model described above to compute the full phase diagrams of chromatin via the Direct Coexistence Simulation method. This will allow me to investigate how changes in linker DNA length, ionic environment, and nucleosome DNA unwrapping influences the critical temperature for phase separation.
O3. To extend the model to account for binding of phase-separating architectural proteins and use it to understand nucleosome organization inside functional chromatin domains. This will allow me to understand how binding of architectural proteins coupled to intrinsic characteristics in chromatin structure influence the phase behaviour of chromatin. We will aim to compare our results using proteins that are correlated with the formation of active, inactive, and repressed domains in mammalian genomes. The understanding gained will be central to propose molecular mechanisms that explain the regulation of nucleosome organization inside structurally different chromatin phase-separated domains.
Organisations
People |
ORCID iD |
| Rosana Collepardo-Guevara (Primary Supervisor) | |
| Esmae Woods (Student) |