Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Friday Speaker Abstracts

THE CROWDED NANOENVIRONMENT INFLUENCES GENE EXPRESSION Anne Shim 1 ; Rikkert J Nap 1,3 ; Luay Almassalha 1 ; Hiroaki Matsuda 1 ; Vadim Backman 1 ; Igal Szleifer 1,2,3 ; 1 Northwestern University, Biomedical Engineering, Evanston, Illinois, United States 2 Northwestern University, Chemistry, Evanston, Illinois, United States 3 Northwestern University, Chemistry of Life Processes Institute, Evanston, Illinois, United States Gene expression is influenced, and perhaps regulated, by the chromatin nanoenvironment. Genes are highly crowded by biological macromolecules, including proteins and non-coding chromatin, which alter the kinetics and efficiency of transcriptional machinery at steady-state. However, owing to processes like chromatin translocation, protein diffusion, and DNA loop extrusion, macromolecular crowders are highly mobile, and the nucleus is almost certainly not at steady- state. Moreover, little is known about how crowding kinetics beyond steady-state integrate with gene expression. Therefore, we investigate, experimentally and computationally, how transcription kinetics are altered by the time-evolving, crowded chromatin nanoenvironment. We conducted a parametric study, whereby temporal changes in crowding density (“dynamic crowding”) were nominated from experimental measurements and incorporated into a computational model of transcription. From experimental studies, ChromEMT quantified physiologically relevant crowding densities that exist in vivo , while Partial Wave Spectroscopic microscopy determined qualitative crowding movement within these densities. These measurements, together with steric and thermodynamic crowding effects determined from Brownian dynamics simulations of diffusion and Monte Carlo simulations of binding free energies, were integrated into a network model of transcription. We show that while transcription is governed by the local average crowding density as shown in previous studies, it also depends critically on the temporal properties of dynamic crowding. Furthermore, dynamic crowding regulates gene expression by influencing the rates of two different components of the transcription pathway-pre-mRNA processing and transcriptional protein search and binding kinetics-at different time points. Therefore, this work demonstrates that macromolecular crowding may play an even greater role in regulating transcription kinetics than previously understood, as it presents crowding kinetics within the bulk chromatin nanoenvironment as a novel regulatory framework for gene expression.

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