A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation - Geng, Yuncong; Bohrer, Christopher Herrick; Yehya, Nicolás; Hendrix, Hunter; Shachaf, Lior; Liu, Jian; Xiao, Jie; Roberts, Elijah (PLoS computational biology, 2022)
Keywords: Binding sites; Biology and life sciences; Cooperation; Deoxyribonucleic acid; Diffusion rate; DNA; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - metabolism; Domains; E coli; Elongation; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Gene expression; Gene Expression Regulation, Bacterial - genetics; Gene regulation; Genes; Genetic aspects; Genetic regulation; Genetic transcription; Genomes; Learning models (Stochastic processes); Medicine and Health Sciences; Physical Sciences; Proteins; Research and Analysis Methods; RNA polymerase; RNA polymerases; Stochastic models; Stochasticity; Structure; Supercoiling; Topology; Transcription; Transcription, Genetic - genetics; Translocation; United States