RNA polymerase II clustering through carboxy-terminal domain phase separation

Abstract

The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is an intrinsically disordered low-complexity region that is critical for pre-mRNA transcription and processing. The CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast. Here we report that human and yeast CTDs undergo cooperative liquid phase separation, with the shorter yeast CTD forming less-stable droplets. In human cells, truncation of the CTD to the length of the yeast CTD decreases Pol II clustering and chromatin association, whereas CTD extension has the opposite effect. CTD droplets can incorporate intact Pol II and are dissolved by CTD phosphorylation with the transcription initiation factor IIH kinase CDK7. Together with published data, our results suggest that Pol II forms clusters or hubs at active genes through interactions between CTDs and with activators and that CTD phosphorylation liberates Pol II enzymes from hubs for promoter escape and transcription elongation.

Phase separation of 53 BP 1 determines liquid‐like behavior of DNA repair compartments

“…Such interactions retain a larger conformational flexibility compared to interactions through complementary protein domain surfaces and induced fit (Aguzzi & Altmeyer, 2016;Boeynaems et al, 2018). Moreover, phase separation occurs at gene promoters and super-enhancers (Boehning et al, 2018;Boija et al, 2018;Lu et al, 2018;Sabari et al, 2018). Moreover, phase separation occurs at gene promoters and super-enhancers (Boehning et al, 2018;Boija et al, 2018;Lu et al, 2018;Sabari et al, 2018).…”

“…Besides the nucleolus, nuclear speckles, and RNA granules, also silent heterochromatin domains were recently shown to phase separate within the nucleus (Larson et al, 2017;Strom et al, 2017). Moreover, phase separation occurs at gene promoters and super-enhancers (Boehning et al, 2018;Boija et al, 2018;Lu et al, 2018;Sabari et al, 2018). To which extent other chromatin domains rely on phase separation for their spatio-temporal confinement and for their biological functions is a matter of intense investigation.…”

Membraneless nuclear organelles and the search for phases within phases

“…It is presently unknown how various multivalent interactions acting together results in self-organization. However, LLPS-like processes likely influence the organization and interaction of most cellular macromolecules, exemplified by the recent evidence that eukaryotic transcription systems, including genome interaction hubs, exhibit selforganizing attributes (Boehning et al, 2018;Cho, Spille, Hecht, et al, 2018;Chong et al, 2018;Lu et al, 2018;Sabari, Dall'Agnese, Boija, et al, 2018). This review will focus on the reported functional architecture of the larger (>1 μm) and well-documented nuclear bodies, such as nucleoli, paraspeckles, and nuclear speckles ( Figure 2).…”

Biomolecular condensates in neurodegeneration and cancer

“…Super‐enhancers are thought to facilitate cancer development by driving a higher transcriptional output of prominent oncogenes . Recent studies demonstrate that IDR‐containing transcription factors, transcriptional coactivators (eg, Mediator complex and Mediator‐associated BRD4) and RNA Polymerase II phase‐separate in vitro . These proteins also assemble liquid‐like condensates at super‐enhancer target genes, activating their expression.…”