The Role of RNA Polymerase II Contiguity and Long-Range Interactions in the Regulation of Gene Expression in Human Pluripotent Stem Cells

Figure 2

Long-range interactions between individual alleles of the selected genes and POU5F1 in hPSCs and early differentiated cells and upon RNAP II inhibition. (a) Analysis of long-range interactions between individual alleles of the selected genes in hPSCs shows that these allelic associations do not change during differentiation and upon RNAP II inhibition. Only RUNX1-RUNX1 allelic association increases from 8.22% to 18.1% with differentiation, and POU5F1-POU5F1 increases from 9.9% to 21.3%. (b) Analysis of long-range interactions between individual alleles of POU5F1 in more detail shows a two-fold increase in long-range interactions during differentiation from 9.9% to 21.3%. Upon RNAP II inhibition, long-range interactions remain stable or show a slight decrease compared to those in control undifferentiated hPSCs. (c) This increase in POU5F1 allele pairing during differentiation cannot be explained by reduction of nuclear size and volume of early differentiated cells. Representative images showing the hiPSC line ID CBIA-19 in passage 35 are shown. Cell nuclei were counterstained with DAPI (blue). Scale bar: 10 μm. For 3D-FISH, at least 500 nuclei for each gene combination were counted (). In the case of POU5F1, . In charts, columns show means and error bars show SEM. Student’s -test, , , and .

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