Disordered Chromatin Packing Regulates Ensemble Gene Expression and Phenotypic Plasticity

Abstract

The adaptive potential of organisms is determined not only by their genetic code, but also by their ability to modulate their transcriptome to create new functional states. Transcription itself is a series of chemical reactions governed by local molecular factors and further modulated by macromolecular crowding, which influences the mobility and kinetics of transcriptional reactants. Within the nucleus the predominant crowder is chromatin, the disordered nucleoprotein polymer which controls packing of the genome. Thus, we hypothesized that the three-dimensional structure of chromatin should have a profound influence on large-scale gene expression patterns. First, we developed a multi-scale computational model which integrates disordered chromatin packing (CP) with local macromolecular crowding (MC) to estimate ensemble gene expression patterns. Microscopy and chromosome conformation capture techniques have demonstrated that, at the level of hundreds of kilobases, chromatin is organized into chromatin packing domains that exhibit fractal, power-law scaling behavior. Our CPMC model considers each of these domains to have their own genomic size, fractal dimension, and average chromatin packing density, which we predict are all physical regulators of gene expression. Next, we experimentally validate the importance of these physical properties of chromatin organization on transcription. Specifically, we utilize a combination of nanoscale-sensitive microscopy techniques to measure chromatin structure, including ChromEM (Chromatin Electron Microscopy) and PWS (Partial WaveSpectroscopic) microscopy, combined with RNA sequencing to measure corresponding gene expression levels. Additionally, we evaluate how chromatin packing influences transcriptional responsiveness of a cell population to an exogenous stressor. Finally, we identify an inverse relationship between cancer patient survival post chemotherapy treatment and phenotypic plasticity of tumor cells as determined by publicly available cancer patient transcriptional data. In summary, we demonstrate the crucial role of supranucleosomal chromatin packing on modulating both large-scale transcription patterns and phenotypic plasticity.