Clr4SUV39H1 and Bdf2BRD4 ubiquitination mediate transcriptional silencing via heterochromatic phase transitions

Abstract

AbstractHeterochromatin has crucial roles in genome stability by silencing repetitive DNA and by suppressing recombination1,2. In the fission yeast Schizosaccharomyces pombe, Clr4 methylates histone H3 lysine 9 (H3K9) to maintain centromeric heterochromatin during the cell cycle, guided by RNA interference (RNAi)3,4. Clr4 interacts with a specialized ubiquitination complex CLRC, which is recruited in part by small RNA and the RNAi transcriptional silencing complex (RITS) but otherwise, the role of CLRC is unknown5–8. Here we show that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and targets Clr4 for mono-ubiquitination at an intrinsically disordered region. Mono-ubiquitination is essential for the transition from co-transcriptional (H3K9me2) to transcriptional (H3K9me3) gene silencing by transiently releasing Clr4 from centromeric heterochromatin, and is reversed by the deubiquitinating enzyme Ubp3. Addition of ubiquitin changes the liquid-liquid phase separation (LLPS) of Clr4 to enhance its dynamic activity. Ubc4-CLRC also poly-ubiquitinates Bdf2, the homologue of BET family double bromodomain protein BRD4 for degradation, which otherwise accumulates at centromeres to promote transcription and production of small RNAs.