Fig. 6: Kinetic model predicts transcriptional change in sox9 gene due to TAD boundary deletion.
From: Predicting gene expression changes from chromatin structure modification
a Schematic of the kinetic model: kcnj2 and sox9 promoters can bind to enhancers with their respective binding and unbinding rates on the genomic location. The transcription factors are represented by spheres which move freely in the nucleoplasm and can bind/unbind with both the promoters; b Validation of the kinetic model. The probability distribution plot of enhancer cluster size around the sox9 promoter in polymer simulation (red curve) and kinetic model (blue curve) is shown; c Relative expression of sox9 in E13.5 limb buds for WT and DELC cells. Bars represent the mean of condensate size and error bars represent the standard deviation. The WT gene expression is normalized to one both for experiment and simulation. For the DELC cell, the blue bar shows the experimental result and the green bar shows the simulation result.
