Interaction of the pioneer transcription factor GATA3 with nucleosomes

Hiroki Tanaka, Yoshimasa Takizawa, Motoki Takaku, Daiki Kato, Yusuke Kumagawa, Sara A. Grimm, Paul A. Wade () and Hitoshi Kurumizaka ()
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Hiroki Tanaka: Institute for Quantitative Biosciences, The University of Tokyo
Yoshimasa Takizawa: Institute for Quantitative Biosciences, The University of Tokyo
Motoki Takaku: National Institute of Environmental Health Sciences
Daiki Kato: Waseda University
Yusuke Kumagawa: Institute for Quantitative Biosciences, The University of Tokyo
Sara A. Grimm: National Institute of Environmental Health Sciences
Paul A. Wade: National Institute of Environmental Health Sciences
Hitoshi Kurumizaka: Institute for Quantitative Biosciences, The University of Tokyo

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract During cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation. Here, we use high-resolution nucleosome mapping in human cells to explore the impact of the position of GATA motifs on the surface of nucleosomes on productive enhancer formation, finding productivity correlates with binding sites located near the nucleosomal dyad axis. Biochemical experiments with model nucleosomes demonstrate sufficiently stable transcription factor-nucleosome interaction to empower cryo-electron microscopy structure determination of the complex at 3.15 Å resolution. The GATA3 zinc fingers efficiently bind their target 5′-GAT-3′ sequences in the nucleosome when they are located in solvent accessible, consecutive major grooves without significant changes in nucleosome structure. Analysis of genomic loci bound by GATA3 during reprogramming suggests a correlation of recognition motif sequence and spacing that may distinguish productivity of new enhancer formation.

Date: 2020
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DOI: 10.1038/s41467-020-17959-y

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