Abstract

Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

* Some experiments were performed according to reviewer's suggestions. DNA methylation analysis in Xenopus egg extracts/mESC, NMR experiments and in vitro ubiquitination assay results have been added in the revised manuscript.

Details

Title
Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger
Author
Hata, Keiichi; Kobayashi, Naohiro; Sugimura, Keita; Qin, Weihua; Deis Haxholli; Chiba, Yoshie; Yoshimi, Sae; Hayashi, Gosuke; Onoda, Hiroki; Ikegami, Takahisa; Mulholland, Christopher B; Nishiyama, Atsuya; Nakanishi, Makoto; Leonhardt, Heinrich; Konuma, Tsuyoshi; Arita, Kyohei
University/institution
Cold Spring Harbor Laboratory Press
Section
New Results
Publication year
2022
Publication date
Oct 4, 2022
Publisher
Cold Spring Harbor Laboratory Press
ISSN
2692-8205
Source type
Working Paper
Language of publication
English
ProQuest document ID
2676400582
Copyright
© 2022. This article is published under http://creativecommons.org/licenses/by-nd/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.