DNA topological regulation by topoisomerase IIbeta-DNA-PK interaction is important for controlled hypoxia-inducible gene expression

Hypoxic stress responses are crucial for cellular and organismal survival and provoke gene regulation in diverse biological pathways including cell cycle progression and energy metabolism. Here, we show that topoisomerase II{beta} (TOP2B) regulates DNA topology and transcription in hypoxia-inducible genes (HIGs) in a DNA-PK-dependent manner. Cellular, mutational, and genomic analyses showed an antagonistic relationship between TOP2B and DNA-PK activities. TOP2B associates with HIGs and represses transcription by suppressing negative supercoiling formation under normoxic conditions. Under hypoxia, TOP2B is released, while DNA-PK and HIF1 are recruited to and activate HIGs. Intriguingly, DNA-PK is responsible for TOP2B to function repressively because DNA-PK knockout overturns both TOP2B release and activity and increases the expression of a number of HIGs. Mutational and genomic analyses confirmed that DNA-PK phosphorylates TOP2B at T1403 to stimulate TOP2B catalysis to suppress the open DNA conformation, which is important for controlled HIG transcription. Collectively, our findings suggest a novel role for TOP2B and DNA-PK-mediated TOP2B regulation as important transcriptional elements in HIG expression. We propose that TOP2B catalysis modulated by protein phosphorylation is coordinated with transcriptional states and determines DNA topology to regulate Pol II transcription.