ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes

Heeyoun Bunch (), Deukyeong Kim, Masahiro Naganuma, Reiko Nakagawa, Anh Cong, Jaehyeon Jeong, Haruhiko Ehara, Hongha Vu, Jeong Ho Chang, Matthew J. Schellenberg and Shun-ichi Sekine
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Heeyoun Bunch: Kyungpook National University
Deukyeong Kim: Kyungpook National University
Masahiro Naganuma: RIKEN Center for Biosystems Dynamics Research
Reiko Nakagawa: RIKEN BDR Laboratory for Phyloinformatics
Anh Cong: Mayo Clinic
Jaehyeon Jeong: Kyungpook National University
Haruhiko Ehara: RIKEN Center for Biosystems Dynamics Research
Hongha Vu: Kyungpook National University
Jeong Ho Chang: Kyungpook National University
Matthew J. Schellenberg: Mayo Clinic
Shun-ichi Sekine: RIKEN Center for Biosystems Dynamics Research

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract The function of the mitogen-activated protein kinase signaling pathway is required for the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth and proliferation. Recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained 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 indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK2 delays TOP2B catalysis of negative DNA supercoiling. In addition, ERK1 may relax DNA supercoiling by itself. ERK2 catalytic inhibition or knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we present the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with the EGR1 transcriptional start site (–30 to +20) that has the strongest affinity to TOP2B within –423 to +332. The structure shows TOP2B-mediated breakage and dramatic bending of the DNA. Transcription is activated by etoposide, while it is inhibited by ICRF193 at EGR1 and FOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.

Date: 2023
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DOI: 10.1038/s41467-023-44089-y

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