(253h) Dewdrops on the Genome: Regulation of Cell-Identity By Biomolecular Phase Transitions

Broader motivation: Human health requires coordination between thousands of cell-types (identities) that all remarkably share an identical genome. A cell’s identity i.e. its ability to perform specific yet diverse functions, is dependent on (a) selective decoding of the genome (gene regulation) (b) spatio-temporal organization into modules (organelles) and (c) interactions with other cell-types and environment (signaling) - inherently spanning multiple scales from genes to tissues. Mistakes or dysregulation in this process underlies improper cellular identity and disease, including cancer, auto-immunity, and degenerative disorders.

Key challenge: Recent research, including work I will describe, has uncovered an important role for phase transitions in cellular function and identity. However, quantitative models of self-organization, including phase transitions, in living systems remain lacking. This is largely due to the complexity involved - cells contain thousands of interacting, reactive components (DNA, RNA, proteins, lipids) present in crowded heterogeneous environments and modulated by active processes that feedback across scales spanning orders of magnitude.

Talk overview: In this talk, I will outline an interdisciplinary and collaborative approach to study phase transitions in cell function and identity at the interface of physics and biology, moored by approaches from chemical engineering. My talk will be focused on three aspects of cell-identity outlined above, through the lens of phase transitions and self-organization:

• Decoding gene regulation: I will introduce our discovery of a key role for phase separation, a physicochemical process, in regulation of mammalian gene expression(1). By integrating coarse-grained simulations, polymer chemistry, and non-equilibrium transport with live-cell and biochemical experiments, I will describe a series of collaborative efforts that revealed features of non-coding regulatory elements (2) and identified an important feedback axes between active RNA synthesis and gene expression (3). I will conclude this section by highlighting ongoing research on the role of gene activity in nuclear organization.
  
  
• Organizing the cell: Phase separation contributes to organizing the cellular milieu into dozens of co-existing compartments containing hundreds of species. Predicting the phase behavior of such complex fluids has remained a daunting task. In this section, I will outline our recent efforts to address this challenge by integrating statistical thermodynamics, numerical simulation, and approaches from random-matrix theory. I will describe how fluids with dozens of components exhibit surprisingly predictable phase behavior (4), even when the underlying component interactions are drawn randomly from a distribution. I will conclude by highlighting ongoing studies on non-equilibrium processes and linking programmed (or evolved) interactions to emergent self-assembly.
  
  
• Interacting cell-circuits: Cells interact with their physiological context to drive signaling that often relies on combinatorial and stochastic cues. In this section, I will describe ongoing collaborations to decipher mechanisms by which cell-types in the sensory system proofread cell-cell connections with high fidelity through self-organization, employing a combination of Monte-Carlo simulations and theory.

Long-term: In the last decade, invention of exciting tools have enabled characterization (sequencing, imaging) and engineering (gene-editing, synthetic biology) of genes and cells - holding great promise for human health and industrial applications. Given the prominent role of self-organization in living systems - I aim to develop quantitative physicochemical models that will provide a rational basis to guide both mechanistic and translational applications of these tools with focus on diseases caused by improper cell-identity. More specifically, in the short-term, I aim to contribute towards the rational design of therapeutics for the expanding list of diseases that are coupled to defects in phase behavior.

References:

1. D. Hnisz=, K. Shrinivas=, R. A. Young, A. K. Chakraborty, P. A. Sharp, A Phase Separation Model for Transcriptional Control. Cell. 169, 13–23 (2017).
2. K. Shrinivas=, B. R. Sabari=, E. L. Coffey, I. A. Klein, A. Boija, A. V. Zamudio, J. Schuijers, N. M. Hannett, P. A. Sharp, R. A. Young, A. K. Chakraborty, Enhancer features that drive formation of transcriptional condensates. Mol. Cell. 75, 549-561.e7 (2019).
3. J. E. Henninger=, O. Oksuz=, K. Shrinivas=, I. Sagi, G. LeRoy, M. M. Zheng, J. O. Andrews, A. V. Zamudio, C. Lazaris, N. M. Hannett, T. I. Lee, P. A. Sharp, I. I. Cissé, A. K. Chakraborty, R. A. Young, RNA-Mediated Feedback Control of Transcriptional Condensates. Cell. 184, 207-225.e24 (2021).
4. K. Shrinivas^c, M. P. Brenner, Phase separation in fluids with many interacting components. Proc. Natl. Acad. Sci. 118 (2021), doi:10.1073/pnas.2108551118.