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Cell Res. 2015 Aug;25(8):911-29. doi: 10.1038/cr.2015.72. Epub 2015 Jun 12.

DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination.

Author information

1
1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Nanosystems Initiative Munich (NIM), Via Manara 7, 21052 Busto Arsizio (VA), Italy.
2
1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Department of Theoretical and Applied Sciences, University of Insubria, Via Manara 7, 21052 Busto Arsizio (VA), Italy.
3
1] Adolf-Butenandt Institute, Ludwig Maximilians University Munich, Schillerstr. 44, 80336 Munich, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy.
4
1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Current address: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
5
1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Current address: Intervet International GmbH, Unterschleissheim, Germany.
6
1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Current address: Department of Chemistry, Ludwig Maximilians University Munich, Germany.
7
Department of Theoretical and Applied Sciences, University of Insubria, Via Manara 7, 21052 Busto Arsizio (VA), Italy.

Abstract

DNMT1 is recruited by PCNA and UHRF1 to maintain DNA methylation after replication. UHRF1 recognizes hemimethylated DNA substrates via the SRA domain, but also repressive H3K9me3 histone marks with its TTD. With systematic mutagenesis and functional assays, we could show that chromatin binding further involved UHRF1 PHD binding to unmodified H3R2. These complementation assays clearly demonstrated that the ubiquitin ligase activity of the UHRF1 RING domain is required for maintenance DNA methylation. Mass spectrometry of UHRF1-deficient cells revealed H3K18 as a novel ubiquitination target of UHRF1 in mammalian cells. With bioinformatics and mutational analyses, we identified a ubiquitin interacting motif (UIM) in the N-terminal regulatory domain of DNMT1 that binds to ubiquitinated H3 tails and is essential for DNA methylation in vivo. H3 ubiquitination and subsequent DNA methylation required UHRF1 PHD binding to H3R2. These results show the manifold regulatory mechanisms controlling DNMT1 activity that require the reading and writing of epigenetic marks by UHRF1 and illustrate the multifaceted interplay between DNA and histone modifications. The identification and functional characterization of the DNMT1 UIM suggests a novel regulatory principle and we speculate that histone H2AK119 ubiquitination might also lead to UIM-dependent recruitment of DNMT1 and DNA methylation beyond classic maintenance.

PMID:
26065575
PMCID:
PMC4528052
DOI:
10.1038/cr.2015.72
[Indexed for MEDLINE]
Free PMC Article

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