Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Nature
2013 Oct 10;5027470:249-53. doi: 10.1038/nature12488.
Show Gene links
Show Anatomy links
Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication.
Nishiyama A
,
Yamaguchi L
,
Sharif J
,
Johmura Y
,
Kawamura T
,
Nakanishi K
,
Shimamura S
,
Arita K
,
Kodama T
,
Ishikawa F
,
Koseki H
,
Nakanishi M
.
???displayArticle.abstract???
Faithful propagation of DNA methylation patterns during DNA replication is critical for maintaining cellular phenotypes of individual differentiated cells. Although it is well established that Uhrf1 (ubiquitin-like with PHD and ring finger domains 1; also known as Np95 and ICBP90) specifically binds to hemi-methylated DNA through its SRA (SET and RING finger associated) domain and has an essential role in maintenance of DNA methylation by recruiting Dnmt1 to hemi-methylated DNA sites, the mechanism by which Uhrf1 coordinates the maintenance of DNA methylation and DNA replication is largely unknown. Here we show that Uhrf1-dependent histone H3 ubiquitylation has a prerequisite role in the maintenance DNA methylation. Using Xenopus egg extracts, we successfully reproduce maintenance DNA methylation in vitro. Dnmt1 depletion results in a marked accumulation of Uhrf1-dependent ubiquitylation of histone H3 at lysine 23. Dnmt1 preferentially associates with ubiquitylated H3 in vitro though a region previously identified as a replication foci targeting sequence. The RING finger mutant of Uhrf1 fails to recruit Dnmt1 to DNA replication sites and maintain DNA methylation in mammalian cultured cells. Our findings represent the first evidence, to our knowledge, of the mechanistic link between DNA methylation and DNA replication through histone H3 ubiquitylation.
Figure 1: xUhrf1- and DNA-replication-dependent DNA methylation and ubiquitylation of H3 at lysine 23 in Xenopus egg extracts. a, Sperm chromatin was incubated with interphase egg extracts containing radiolabelled S-[methyl-3H]-adenosyl-L-methionine. His6âgeminin, glutathione S-transferaseâp27 or aphidicolin (APD, 150âµM) was added to the extracts 10âmin before the addition of sperm DNA. After 1âh, sperm DNA was purified from the egg extracts and the incorporation of radioactivity was measured using a scintillation counter. Data shown are representative of three independent experiments. b, Interphase egg extracts immunodepleted (ID) with the indicated antiserum were incubated with sperm nuclei. Extracts and sperm chromatin isolated at the indicated times were analysed by immunoblotting (IB) using the indicated antibodies. c, Chromatin fractions from interphase extracts immunodepleted with the indicated antibodies were isolated at the indicated times after sperm addition and analysed by immunoblotting. d, Chromatin fractions from the indicated immunodepleted extracts were solubilized by MNase and immunoprecipitated with anti-H3 antibodies after treatment with 1% SDS. The resultant immunoprecipitates were subjected to immunoblotting using the indicated antibodies. e, The electron transfer dissociation MS/MS spectrum of the xH3 peptide shows ubiquitylation at lysine 23. Detailed information is provided in Methods. f, Buffer alone (â), recombinant His8-tagged wild-type (WT) rmDnmt1, or its catalytic mutant (cat) proteins (10ângâμlâ1) were added to xDnmt1-depleted extracts. Chromatin fractions isolated at the indicated times were subjected to immunoblotting using the indicated antibodies.
Achour,
The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression.
2008, Pubmed
Achour,
The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression.
2008,
Pubmed
Alabert,
Chromatin replication and epigenome maintenance.
2012,
Pubmed
Arita,
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.
2008,
Pubmed
Arita,
Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1.
2012,
Pubmed
Avvakumov,
Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.
2008,
Pubmed
Bird,
DNA methylation patterns and epigenetic memory.
2002,
Pubmed
Bostick,
UHRF1 plays a role in maintaining DNA methylation in mammalian cells.
2007,
Pubmed
Chen,
High-efficiency transformation of mammalian cells by plasmid DNA.
1987,
Pubmed
Citterio,
Np95 is a histone-binding protein endowed with ubiquitin ligase activity.
2004,
Pubmed
Daigo,
The proteomic profile of circulating pentraxin 3 (PTX3) complex in sepsis demonstrates the interaction with azurocidin 1 and other components of neutrophil extracellular traps.
2012,
Pubmed
Felle,
The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.
2011,
Pubmed
Fujinoki,
Identification of 36-kDa flagellar phosphoproteins associated with hamster sperm motility.
2003,
Pubmed
Hashimoto,
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
2008,
Pubmed
Hu,
Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2.
2011,
Pubmed
Jenkins,
Critical role of the ubiquitin ligase activity of UHRF1, a nuclear RING finger protein, in tumor cell growth.
2005,
Pubmed
Jones,
Rethinking how DNA methylation patterns are maintained.
2009,
Pubmed
Karagianni,
ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation.
2008,
Pubmed
Keller,
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
2002,
Pubmed
Kim,
Systematic and quantitative assessment of the ubiquitin-modified proteome.
2011,
Pubmed
Leonhardt,
A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.
1992,
Pubmed
Lutzmann,
MCM9 binds Cdt1 and is required for the assembly of prereplication complexes.
2008,
Pubmed
,
Xenbase
Margueron,
Chromatin structure and the inheritance of epigenetic information.
2010,
Pubmed
Muraki,
Essential roles of Xenopus TRF2 in telomere end protection and replication.
2011,
Pubmed
,
Xenbase
Nady,
Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.
2011,
Pubmed
Nesvizhskii,
A statistical model for identifying proteins by tandem mass spectrometry.
2003,
Pubmed
Nishiyama,
MCM-BP regulates unloading of the MCM2-7 helicase in late S phase.
2011,
Pubmed
,
Xenbase
Peng,
A proteomics approach to understanding protein ubiquitination.
2003,
Pubmed
Plechanovová,
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.
2012,
Pubmed
Probst,
Epigenetic inheritance during the cell cycle.
2009,
Pubmed
Rajakumara,
PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression.
2011,
Pubmed
Rothbart,
Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation.
2012,
Pubmed
Sharif,
The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA.
2007,
Pubmed
Shimamura,
Interaction between DNMT1 and DNA replication reactions in the SV40 in vitro replication system.
2008,
Pubmed
Song,
Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
2011,
Pubmed
Takebayashi,
Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions.
2007,
Pubmed
