Abstract
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid–liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super‐resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid‐phase condensation at concentrations that are too low for canonical liquid–liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface‐associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.
Highlights
Eukaryotic cells have an extensive library of genetic DNA sequences at their disposal, but selectively transcribe only a small subset of this genetic information into RNA transcripts at any given point in time
These morphology types seem to correlate with different levels of polymerase II (Pol II) Ser5P and Pol II Ser2P signal. (Note that the Pol II carboxy-terminal domain (CTD) YSPTSPS motif is repeated 52 times per Pol II complex in zebrafish, implying that (i) fluorescence intensity is not necessarily directly proportional to molecule numbers, and (ii) signal is amplified, so that spots might correspond to single genes, or even single polymerases.) Type i clusters are small, appear as dots in the Pol II Ser5P channel, and exhibit low Pol II Ser2P signal
We investigated how recruited and elongating Pol II contribute to the morphology of macromolecular clusters enriched in Pol II
Summary
Eukaryotic cells have an extensive library of genetic DNA sequences at their disposal, but selectively transcribe only a small subset of this genetic information into RNA transcripts at any given point in time. Two major points at which transcription by Pol II is controlled are initiation and pause release (Bartman et al, 2019). After proceeding for 20– 60 base pairs along the DNA sequence, initiated Pol II complexes enter a state of promoter-proximal pausing (Adelman & Lis, 2012). The rates of Pol II initiation and subsequent release from the paused state are under cellular control and can differ between genes and change in response to stimuli (Gressel et al, 2017; Bartman et al, 2019). When pause release is slower than initiation, Pol II remains in the promoterproximal position, entering the so-called poised state. Some genes are poised—supposedly in preparation for subsequent expression during cell type specification (Chen et al, 2013; GhaviHelm et al, 2014)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
