DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [TMP-seq]

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 identified that topoisomerase IIβ (TOP2B) regulates DNA topology and transcription in hypoxiainducible genes (HIGs) in a DNA-PK-dependent manner. Cellular, mutational, and genomic analyses showed antagonistic relation between TOP2B and DNA-PK. TOP2B associates with HIGs and represses transcription by suppressing negative supercoiling formation under normoxic conditions.Under hypoxia, TOP2B is released, whereas DNA-PK and HIF1a are recruited to and activate HIGs.Intriguingly, DNA-PK is responsible for TOP2B to be repressive because DNA-PK knockout overturns both TOP2B activity and release 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 for DNA topological relaxation, which is important for controlled HIG transcription. Collectively, our findings suggest a novel role of 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 activation and determines DNA topology to stimulate Pol II transcription in response to hypoxic stresses. TMP-seq data from SH-SY5Y cells were generated. The samples consist of wild-type (WT), TOP2B knockout (KO), and TOP2B mutant-expressing SH-SY5Y cells, with and without CoCl2-induced hypoxic stress. Each condition was prepared in biological triplicates to ensure reproducibility and reliability.