2016/04/11 by Davide Michieletto, Michieletto, Davide, Davide Marenduzzo +3
Biochemistry, Genetics and Molecular Biology · #Biological Physics (physics.bio-ph) #FOS: Biological sciences #FOS: Physical sciences #Genomics and Chromatin Dynamics #RNA Research and Splicing #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft) #Subcellular Processes (q-bio.SC)
paper · pdf · doi:10.48550/arxiv.1604.03041
openalex publication_date 2016/04/11 · openalex created_date 2022/10/01 · openalex updated_date 2026/07/28
Three-dimensional interphase organization of metazoan genomes has been linked\nto cellular identity. However, the principles governing 3D interphase genome\narchitecture and its faithful transmission through disruptive events of\ncell-cycle, like mitosis, are not fully understood. By using Brownian dynamics\nsimulations of Drosophila chromosome 3R up to time-scales of minutes, we show\nthat chromatin binding profile of Polycomb-repressive-complex-1 robustly\npredicts a sub-set of topologically associated domains (TADs), and inclusion of\nother factors recapitulates the profile of all TADs, as observed\nexperimentally. Our simulations show that chromosome 3R attains interphase\norganization from mitotic state by a two-step process in which formation of\nlocal TADs is followed by long-range interactions. Our model also explains\nstatistical features and tracks the assembly kinetics of polycomb subnuclear\nclusters. In conclusion, our approach can be used to predict structural and\nkinetic features of 3D chromosome folding and its associated proteins in\nbiological relevant genomic and time scales.\n