BMI1–UBR5 axis regulates transcriptional repression at damaged chromatin

Abstract

BMI1 is a component of the Polycomb Repressive Complex 1 (PRC1), which plays a key role in maintaining epigenetic silencing during development. BMI1 also participates in gene silencing during DNA damage response, but the precise downstream function of BMI1 in gene silencing is unclear. Here we identified the UBR5 E3 ligase as a downstream factor of BMI1. We found that UBR5 forms damage-inducible nuclear foci in a manner dependent on the PRC1 components BMI1, RNF1 (RING1a), and RNF2 (RING1b). Whereas transcription is repressed at UV-induced lesions on chromatin, depletion of the PRC1 members or UBR5 alone derepressed transcription elongation at these sites, suggesting that UBR5 functions in a linear pathway with PRC1 in inducing gene silencing at lesions. Mass spectrometry (MS) analysis revealed that UBR5 associates with BMI1 as well as FACT components SPT16 and SSRP1. We found that UBR5 localizes to the UV-induced lesions along with SPT16. We show that UBR5 ubiquitinates SPT16, and depletion of UBR5 or BMI1 leads to an enlargement of SPT16 foci size at UV lesions, suggesting that UBR5 and BMI1 repress SPT16 enrichment at the damaged sites. Consistently, depletion of the FACT components effectively reversed the transcriptional derepression incurred in the UBR5 and BMI1 KO cells. Finally, UBR5 and BMI1 KO cells are hypersensitive to UV, which supports the notion that faulty RNA synthesis at damaged sites is harmful to the cell fitness. Altogether, these results suggest that BMI1 and UBR5 repress the polymerase II (Pol II)-mediated transcription at damaged sites, by negatively regulating the FACT-dependent Pol II elongation.erturbation of chromatin structures can cause inappropriate gene expression and loss of genome integrity. Polycomb proteins are recognized in all metazoans for their conserved transcriptional repressive function. The canonical Polycomb Repressive Complex 1 (PRC1) contains BMI1, RNF1 (RING1a), RNF2 (RING1b), core components (PC), Polyhomeotic (PH), and CBX proteins (1, 2). BMI1 serves as a key regulatory component of the PRC1 complex, which is required to maintain the transcriptionally repressed state of many genes throughout development via chromatin remodeling and histone modification (1). The only known enzymatic activity of the BMI1-containing PRC1 complex is to monoubiquitinate histone H2A at Lys-119 (K119) residue, which is associated with transcriptional repression (1, 3, 4). However, the E3 ubiquitin ligase activity of RNF2 or the H2AK119-Ub is dispensable for repression of canonical PRC1 target genes during mouse or Drosophila embryonic development, respectively (5, 6), suggesting that the PRC1 complex may also induce gene silencing through other mechanisms (7). A series of studies has suggested that multiple distinct forms of the PRC1 complex with varying components could exist, and each of these may have distinct modes of regulation and functions (reviewed in ref. 2).In addition to its well-known role as an oncogene, recent evidence suggests that BMI1 participates in the DNA damage res...

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