The role of RNA Polymerase II contiguity and long-range interactions in the regulation of gene expression in human pluripotent stem cells.

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Authors

EISELLEOVÁ Lívia LUKJANOV Viktor FARKAŠ Šimon SVOBODA David ŠTĚPKA Karel KOUTNÁ Irena

Year of publication 2019
Type Article in Periodical
Magazine / Source Stem Cells International
MU Faculty or unit

Faculty of Informatics

Citation
Web http://dx.doi.org/10.1155/2019/1375807
Doi http://dx.doi.org/10.1155/2019/1375807
Keywords human pluripotent stem cells; RNA polymerase II; transcription factors; transcription factories; long-range interactions; early differentiation
Attached files
Description In this study, we examined long-range interactions between the POU5F1 gene and genes previously identified as being POU5F1 enhancer-interacting, namely, CDYL, TLE2, RARG, and MSX1 (all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene, we used RUNX1, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions between POU5F1 and the selected genes change with the onset of differentiation and upon RNAP II inhibition, we performed three-dimensional fluorescence in situ hybridization (3D-FISH) followed by computational simulation analysis. Our analysis showed that the numbers of long-range interactions between specific genes decrease during differentiation, suggesting that the transcription of monitored genes is associated with pluripotency. In addition, we showed that upon inhibition of RNAP II, long-range associations do not disintegrate and remain constant. We also analyzed the distance distributions of these genes in the context of their positions in the nucleus and revealed that they tend to have similar patterns resembling normal distribution. Furthermore, we compared data created in vitro and in silico to assess the biological relevance of our results.
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