RNA polymerase II (Pol II)-dependent transcription in stimulus-inducible genes requires topoisomerase IIβ (TOP2B)-mediated DNA strand break and the activation of DNA damage response signalling in humans. Here, we report a novel function of the breast cancer 1 (BRCA1)-BRCA1-associated ring domain 1 (BARD1) complex in this process. We found that BRCA1 is phosphorylated at S1524 by the kinases ataxia-telangiectasia mutated and ATR during gene activation, and that this event is important for productive transcription. Our biochemical and genomic analyses showed that the BRCA1-BARD1 complex interacts with TOP2B in the EGR1 transcription start site and in a large number of protein-coding genes. Intriguingly, the BRCA1-BARD1 complex ubiquitinates TOP2B, which stabilizes TOP2B binding to DNA while BRCA1 phosphorylation at S1524 controls the TOP2B ubiquitination by the complex. Together, these findings suggest the novel function of the BRCA1-BARD1 complex in the regulation of TOP2B and Pol II-mediated gene expression.

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Transcription of stress-inducible genes requires synchronized and robust activation, which is critical for organismal survival and homeostasis. The function of mitogen-activated protein kinase (MAPK) signaling pathway is involved in the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth1-3. In addition, recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation in IEGs4-6. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation remains unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at the EGR1 gene. Our data indicated that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Inhibition of ERK2 kinase activity or ERK2 knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, the cryo-EM structure of the TOP2B-EGR1 transcription start site-etoposide complex demonstrated breakage and dramatic bending of the double-stranded DNA, suggesting the mechanism of TOP2B-mediated transcriptional activation. Taken together, this study suggests that the activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions during transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be important for the dissociation step.