Transcriptional suppression of ribosomal DNA with phase separation
Satoru Ide, Ryosuke Imai, Hiroko Ochi, and Kazuhiro Maeshima
Science Advances 6,eabb5953(2020) DOI:10.1126/sciadv.abb5953
The nucleolus is a nuclear body with multiphase liquid droplets for ribosomal RNA (rRNA) transcription. How rRNA transcription is regulated in the droplets remains unclear. Here, using single-molecule tracking of RNA polymerase I (Pol I) and chromatin-bound upstream binding factor (UBF), we reveal suppression of transcription with phase separation. For transcription, active Pol I formed small clusters/condensates that constrained rDNA chromatin in the nucleolus fibrillar center (FC). Treatment with a transcription inhibitor induced Pol I to dissociate from rDNA chromatin and to move like a liquid within the nucleolar cap that transformed from the FC (Fig. 1). Expression of a Pol I mutant associated with a craniofacial disorder inhibited transcription by competing with wild-type Pol I clusters and transforming the FC into the nucleolar cap (Fig. 2). The cap droplet excluded an initiation factor, ensuring robust silencing. Our findings suggest a mechanism of rRNA transcription suppression via phase separation of intranucleolar molecules governed by Pol I.
This work was supported by the Japan Society for the Promotion of Science KAKENHI grants (15K18580, 15H01361, and 18K06187 to S.I.; 16H04746 and 19H05273 to K.M.), a Japan Science and Technology Agency CREST grant (JPMJCR15G2 to K.M.), and the Takeda Science Foundation (to K.M.).
Fig. 1. Diagram of nucleolar reorganization in response to transcription inhibition through phase separation. Left: In the nucleolus fibrillar center (FC, dark blue), active Pol I molecules (pink) form a stable cluster/condensate to transcribe rRNA genes (rDNA), constraining rDNA chromatin. Right: Once transcription is inhibited by a drug, the FC components segregate to the nucleolar periphery, where they coalesce to form large bodies called nucleolar caps. The Pol I cluster/condensate detaches from chromatin, thus releasing the chromatin constraint. Pol I and rDNA behave like a liquid in the nucleolar cap through further phase separation.
Fig. 2. Suppression of transcription with phase separation by a mutant Pol I associated with a craniofacial disorder. Mutant Pol I stably binds to rDNA chromatin and inhibits wild-type Pol I cluster/condensate formation (middle). The whole Pol I population becomes mobile in the nucleolar cap. A transcription initiation factor (violet) is excluded from the cap droplet, ensuring robust transcription suppression within the cap (middle). This process can cause the failure of ribosome biogenesis on craniofacial skeletal development in a patient (right, the image given by Dr. K. Nicole Weaver in Cincinnati Children’s Hospital Medical Center).