Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.

Cheng, Jingdong; Yang, Huirong; Fang, Jian; Ma, Lixiang; Gong, Rui; Wang, Ping; Li, Ze; Xu, Yanhui

doi:10.1038/ncomms8023

Cited by 165Epigenetics and DNA MethylationUbiquitin and proteasome pathwaysCancer-related gene regulation

Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.

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Cheng, Jingdong, Yang, Huirong, Fang, Jian, Ma, Lixiang, Gong, Rui, Wang, Ping, Li, Ze, Xu, Yanhui·2015·Nature Communications

DOI 10.1038/ncomms8023PMC PMC4432644

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Abstract

DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues within DNMT1’s KG linker. This intermolecular interaction is required for USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine residues impair DNMT1–USP7 interaction and promote the degradation of DNMT1. Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and decreased total DNMT1 protein. This negative correlation is observed in differentiated neuronal cells and pancreatic cancer cells. Our studies reveal that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide a structural basis for the design of inhibitors, targeting the DNMT1–USP7 interaction surface for therapeutic applications.

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The UBL 1-2 domains contain the second major substrate recognition site for USP7 substrates.
“Outside of the TRAF-like domain, the UBL 1–2 domains contain the second major substrate recognition site for USP7 substrates.”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Cheng et al., 2015
The UBL 1-2 acidic interface interacts with a highly basic motif (R/KxKxxxK) within USP7 substrates including UHRF1, DNMT1 and RNF169.
“This acidic interface interacts with a highly basic motif (R/KxKxxxK) within USP7 substrates that include UHRF1 (Zhang et al., 2015), DNMT1 (Cheng et al., 2015) and RNF169 (An et al., 2017; Figure 1 and Table 1).”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Cheng et al., 2015

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Self-citation

Authors: Cheng, J., Yang, H., Fang, J., Ma, L., Gong, R., Wang, P., Li, Z., & Xu, Y.
Affiliations: Shanghai Medical College of Fudan University (CN)
Corresponding author: Xu, Yanhui
ORCID: Cheng, Jingdong
Yang, Huirong
Fang, Jian
Ma, Lixiang
Gong, Rui
Wang, Ping
Li, Ze
Xu, Yanhui
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2015-05-11
Volume: 6
Issue: 1
Pages: 7023-7023
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/ncomms8023
PMC: PMC4432644
OpenAlex: W2227012542
Cited by: 158
References: 52
Citations by year: 2026: 9 · 2025: 14 · 2024: 10 · 2023: 15 · 2022: 17 · 2021: 14 · 2020: 19 · 2019: 22 · 2018: 18 · 2017: 10 · 2016: 9 · 2015: 1
FWCI: 5.50
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature Communications (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Salt Science Research Foundation
National Natural Science Foundation of China (91419301, U1432242, 31270779, 31425008, 31100526)
Fudan University
Science and Technology Commission of Shanghai Municipality
Program of Shanghai Subject Chief Scientist
National Key Research and Development Program of China (2011CB965300)
National Key New Drug Creation and Manufacturing Program, Ministry of Science and Technology (2014ZX09507-002)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
Keywords: DNMT1, USP7, protein acetylation, protein stabilization, protein-protein interaction, DNA methylation, epigenetic regulation, lysine acetylation, histone deacetylase inhibitors, protein degradation, crystal structure, neurons, pancreatic cancer cells
MeSH terms: Ubiquitin-Specific Peptidase 7, Acetylation, Crystallization, Gene Expression Regulation, Humans, Models, Molecular, Mutation, Protein Conformation, Repressor Proteins, Ubiquitin Thiolesterase, Cell Line, Tumor

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Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.

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