title: Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells.
abstract: Genome sequences provide the overall genetic blueprint of cells, but cells possessing the same genome can exhibit diverse phenotypes. There is a multitude of mechanisms controlling cellular epigenetic states and that dictate the behavior of cells. Among these, networks of interacting molecules, often under stochastic control, depending on the specific wirings of molecular components and the physiological conditions, can have a different landscape of cellular states. In addition, chromosome folding in three-dimensional space provides another important control mechanism for selective activation and repression of gene expression. Fully differentiated cells with different properties grow, divide, and interact through mechanical forces and communicate through signal transduction, resulting in the formation of complex tissue patterns. Developing quantitative models to study these multi-scale phenomena and to identify opportunities for improving human health requires development of theoretical models, algorithms, and computational tools. Here we review recent progress made in these important directions.
authors.affiliation: Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
authors.affiliation: Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
authors.forename: Youfang
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA.
authors.forename: Gamze
authors.initials: G
authors.lastname: Gursoy
authors.affiliation: Toyota Technological Institute at Chicago, 6045 S. Kenwood Ave. Chicago, Illinois 60637, USA.
authors.forename: Hammad
authors.initials: H
authors.lastname: Naveed
authors.affiliation: Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Terebus
authors.affiliation: Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA.
authors.forename: Jieling
authors.initials: J
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D002454:Cell Differentiation / Q000235:genetics*; D002467:Cell Nucleus; D002843:Chromatin / Q000737:chemistry*; D044127:Epigenesis, Genetic / Q000502:physiology*; D005786:Gene Expression Regulation; D006801:Humans; D008954:Models, Biological; D009024:Morphogenesis / Q000235:genetics*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D015398:Signal Transduction
chemical_list: D002843:Chromatin