Bin Zhang

TL;DR: A theoretical model that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is reported that supports the viability of the proposed physical mechanism of chromatin folding and makes the computational model a powerful tool for future investigations.

TL;DR: An energy landscape model of the chromosome is presented that reproduces a diverse set of experimental measurements and enables quantitative predictions of chromosome structure and topology and provides mechanistic insight into the role of 3D genome organization in gene regulation and cell differentiation.

TL;DR: An approximation is developed that allows the quantitative construction of the epigenetic landscape for large realistic model networks and explains many experimental observations, including the heterogeneous distribution of the transcription factor Nanog and its role in safeguarding the stem cell pluripotency.

TL;DR: Analysis of the model’s energy function uncovers distinct mechanisms for chromatin folding at various length scales and suggests a need to go beyond simple A/B compartment types to predict specific contacts between regulatory elements using polymer simulations.

TL;DR: It is found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors and reorganization is accompanied by compartment-specific hypomethylation and chromatin changes.