Geometric and computational models of chromatin fibre folding for human embryonic stem cells

In this study we analyze the chromatin state of human pluripotent stem cells by geometric and computational modelling of fibre conformation. The model takes into account local structure of chromatin organized into euchromatin, permissive for gene activation, and heterochromatin, transcriptionally silenced. Euchromatin was modelled using linear DNA while heterochromatin by means of a solenoid structure in which DNA winds onto six nucleosome spools per turn. Two geometric models are presented and are compared in terms of geometric quantities. The models are tested using in vivo data generated from chromatin human immunoprecipitation from embryonic stem cells. This study provides insight for identifying the relationships between chromosome geometry and epigenomic processes associated with chromatin remodeling, cellular reprograming and maintenance of cellular pluripotency.