DNA-induced spatial entrapment of general transcription machinery can stabilize gene expression in a nondividing cell.


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Article
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Authors
Javed, Khayam 
Jullien, Jerome 
Agarwal, Gaurav 
Lawrence, Nicola 
Butler, Richard 
Abstract

An important characteristic of cell differentiation is its stability. Only rarely do cells or their stem cell progenitors change their differentiation pathway. If they do, it is often accompanied by a malfunction such as cancer. A mechanistic understanding of the stability of differentiated states would allow better prospects of alleviating the malfunctioning. However, such complete information is yet elusive. Earlier experiments performed in Xenopus oocytes to address this question suggest that a cell may maintain its gene expression by prolonged binding of cell type-specific transcription factors. Here, using DNA competition experiments, we show that the stability of gene expression in a nondividing cell could be caused by the local entrapment of part of the general transcription machinery in transcriptionally active regions. Strikingly, we found that transcriptionally active and silent forms of the same DNA template can stably coexist within the same nucleus. Both DNA templates are associated with the gene-specific transcription factor Ascl1, the core factor TBP2, and the polymerase II (Pol-II) ser5 C-terminal domain (CTD) phosphorylated form, while Pol-II ser2 CTD phosphorylation is restricted to the transcriptionally dominant template. We discover that the active and silent DNA forms are physically separated in the oocyte nucleus through partition into liquid-liquid phase-separated condensates. Altogether, our study proposes a mechanism of transcriptional regulation involving a spatial entrapment of general transcription machinery components to stabilize the active form of a gene in a nondividing cell.

Description

Funder: Wellcome Trust

Keywords
Ascl1, Xenopus oocyte, liquid–liquid phase separation, stable gene expression, transcriptional regulation, Animals, Cell Differentiation, DNA, Gene Expression Regulation, Humans, Oocytes, Phosphorylation, RNA Polymerase II, Templates, Genetic, Transcription, Genetic, Xenopus
Journal Title
Proc Natl Acad Sci U S A
Conference Name
Journal ISSN
0027-8424
1091-6490
Volume Title
119
Publisher
Proceedings of the National Academy of Sciences
Sponsorship
Cancer Research UK (C6946/A24843)
Wellcome Trust (203144/Z/16/Z)
Wellcome Trust (203144/A/16/Z)