Open AccessRNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Author(s) -
Pancholi Agnieszka,
Klingberg Tim,
Zhang Weichun,
Prizak Roshan,
Mamontova Irina,
Noa Amra,
Sobucki Marcel,
Kobitski Andrei Yu,
Nienhaus Gerd Ulrich,
Zaburdaev Vasily,
Hilbert Lennart
Publication year - 2021
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.202110272
Subject(s) - chromatin , biology , rna polymerase ii , rna polymerase iii , rna polymerase , transcription (linguistics) , rna , microbiology and biotechnology , dna , biophysics , transcriptional regulation , polymerase , gene , genetics , promoter , gene expression , linguistics , philosophy
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.