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

Autor: Simon Farkas, Lívia Eiselleová, David Svoboda, Viktor Lukjanov, Karel Stepka, Irena Koutná
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Zdroj: Stem Cells International, Vol 2019 (2019)
Stem Cells International
ISSN: 1687-9678
Popis: The eukaryotic nucleus is a highly complex structure that carries out multiple functions primarily needed for gene expression, and among them, transcription seems to be the most fundamental. Diverse approaches have demonstrated that transcription takes place at discrete sites known as transcription factories, wherein RNA polymerase II (RNAP II) is attached to the factory and immobilized while transcribing DNA. It has been proposed that transcription factories promote chromatin loop formation, creating long-range interactions in which relatively distant genes can be transcribed simultaneously. In this study, we examined long-range interactions between thePOU5F1gene and genes previously identified as beingPOU5F1enhancer-interacting, namely,CDYL,TLE2,RARG, andMSX1(all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene,RUNX1was used, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions betweenPOU5F1and 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 createdin vitroand in silico to assess the biological relevance of our results.
Databáze: OpenAIRE
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