Fig. 5: The formation of 3D hubs of active chromatin triggers dynamic gene activation. | Nature Communications

Fig. 5: The formation of 3D hubs of active chromatin triggers dynamic gene activation.

From: Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

Fig. 5

a Correlations between structural features of the models and expression of the resident genes. Each of the seven panels show the scatter-plot, the linear regression model fit line, and the 95% confidence interval between expression (log(RPKM + 1)) with respect number of APD particles, number of AP particles, TSS distance to the closer border, number of A particles, explored (convex-hull) volume, structural embedding and TSS-TTS distance, respectively. The linear regression r coefficient and p-values, that are shown on top of each scatterplot, have been computed using Python (RegPlot function of the seaborn package). b Dynamic changes of the distance to the Sox2 locus TSS for each APD (red), AP (orange) and A (yellow) particles during reprogramming simulation. c Snapshots of the dynamic simulation of the Sox2 locus simulation with the chromatin represented as a cyan ribbon with the Sox2 locus TSS as a black sphere and all APD, AP and A particles as red, orange, and yellow spheres, respectively.

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