Chromatin Scaling and the Regulation of Cellular FunctionPublic Deposited
Chromatin organization involves a hierarchy of length scales ranging from a few tens of nanometers in nucleosomes to hundreds of nanometers for chromosomal territories. This physical nanostructure is regulated by the genetic code, differential methylation and histone modifications that comprise the histone code, as well as non-molecular factors, such as crowding, ionic conditions, and pH. We have developed a novel optical spectroscopic microscopy technique, live cell Partial Wave Spectroscopic (PWS) microscopy, which allows us to interrogate the structure-function relationship of chromatin between 20 and 350 nm in critical processes including DNA repair, replication, transcription, cell cycle, and proliferation. We have demonstrated, both computationally and experimentally, that the physico-chemical regulation of chromatin packing scaling, as measured by PWS, can be used to manipulate transcriptional diversity, intercellular heterogeneity, and gene network heterogeneity. Here we use PWS microscopy and complementary biological assays to show the driving force of chromatin scaling and its regulation in the context of several biological applications including cardiovascular inflammation, stem cell plasticity, and carcinogenesis and chemoevasion. We show that controlling the physicochemical environment within the cellâ€™s nucleus to alter chromatin scaling can predictably modulate global patterns in gene expression. This whole-transcriptome manipulation based on the control of the physiochemical nanoenvironment of chromatin has implications in these as well as essentially any disease state and may allow for the ability to control the overall behavior of biological systems.