Chromatin methylation is necessary for stable repression of gene expression during mammalian development. During cell division, DNMT1 maintains the DNA methylation pattern of the newly synthesized daughter strand, while G9a methylates H3K9. Here, DNMT1 is shown to directly bind G9a both in vivo and in vitro and to colocalize in the nucleus during DNA replication. The complex of DNMT1 and G9a colocalizes with dimethylated H3K9 (H3K9me2) at replication foci. Similarly, another H3K9 histone methyltransferase, SUV39H1, colocalizes with DNMT1 on heterochromatic regions of the nucleoli exclusively before cell division. Both DNMT1 and G9a are loaded onto the chromatin simultaneously in a ternary complex with loading factor PCNA during chromatin replication. Small interfering RNA (siRNA) knockdown of DNMT1 impairs DNA methylation, G9a loading, and H3K9 methylation on chromatin and rDNA repeats, confirming DNMT1 as the primary loading factor. Additionally, the complex of DNMT1 and G9a led to enhanced DNA and histone methylation of in vitro assembled chromatin substrates. Thus, direct cooperation between DNMT1 and G9a provides a mechanism of coordinated DNA and H3K9 methylation during cell division.[Keywords: DNMT1; G9a; SUV39H1; methylation; chromatin; replication] Supplemental material is available at http://www.genesdev.org.

Inheritance of epigenetic information encoded by cytosine DNA methylation patterns is crucial for mammalian cell survival, in large part through the activity of the maintenance DNA methyltransferase (DNMT1). Here, we show that SET7, a known histone methyltransferase, is involved in the regulation of protein stability of DNMT1. SET7 colocalizes and directly interacts with DNMT1 and specifically monomethylates Lys-142 of DNMT1. Methylated DNMT1 peaks during the S and G 2 phases of the cell cycle and is prone to proteasome-mediated degradation. Overexpression of SET7 leads to decreased DNMT1 levels, and siRNA-mediated knockdown of SET7 stabilizes DNMT1. These results demonstrate that signaling through SET7 represents a means of DNMT1 enzyme turnover.DNA methyltransferase ͉ methylated lysine ͉ proteasome ͉ protein degradation M ammalian DNA methylation is essential for development and is controlled by a variety of factors including 3 active DNA cytosine methyltransferases (DNMT1, DNMT3A, and DNMT3B) and a methyltransferase-like protein, DNMT3L (1-4). DNMT1 encodes the maintenance DNA methyltransferase (DNMT) responsible for methylating hemimethylated CpG sites shortly after DNA replication, and it is assisted by an accessory factor capable of recognizing hemimethylated DNA called UHRF1 (5, 6). Aberrant DNA methylation of CpG islandcontaining promoters leads to permanent silencing of genes in both physiological and pathological contexts and specifically in cancer cells (7). In cancer cells, disruption of DNMT1 resulted in hemimethylation of a fifth of the CpG sites in the genome and activation of the G 2 /M checkpoint, leading to arrest in the G 2 phase of the cell cycle (8). Apart from DNA methylationmediated gene silencing, DNMT1 also binds to several transcriptional inhibitors and represses gene expression in a DNA methylation-independent manner (9-11). Pharmacological inhibitors of DNMT1 [5-azacytidine (5-aza-CR) and its deoxy analog, 5-aza-2Ј-deoxycytidine (5-aza-CdR)] get incorporated into newly-synthesized DNA (12, 13). Once incorporated into DNA, these compounds form covalent complexes with DNMTs, thereby depleting active enzymes (14, 15) and activating gene expression (16). Recently, 5-aza-CdR-induced depletion of DNMT1 was shown to be mediated by proteasomal pathways in mammalian nuclei (17). However, little is known about other factors regulating DNMT1 levels in cells. Here, we show that DNMT1 stability is regulated by protein methylation coupled to proteasome-mediated protein degradation through the protein methyltransferase activity of SET7. Results DNMT1 Colocalizes and Associates with and Is Methylated by SET7.We used gel filtration and Western blot analysis to analyze DNMT1 from nuclear extracts. Using a highly-specific antibody we observed a major species of DNMT1 at 185 kDa and a higher molecular mass minor species (Fig. 1A). It seemed likely that this minor species of DNMT1 may be posttranslationally modified (18). To test whether DNMT1 might be modified by protein methylation, recombinant DNMT1 wa...

The protein lysine methyltransferase SET7 regulates DNA methyltransferase-1 (DNMT1) activity in mammalian cells by promoting degradation of DNMT1 and thus allows epigenetic changes via DNA demethylation. Here we reveal an interplay between monomethylation of DNMT1 Lys142 by SET7 and phosphorylation of DNMT1 Ser143 by AKT1 kinase. These two modifications are mutually exclusive, and structural analysis suggests that Ser143 phosphorylation interferes with Lys142 monomethylation. AKT1 kinase colocalizes and directly interacts with DNMT1 and phosphorylates Ser143. Phosphorylated DNMT1 peaks during DNA synthesis, before DNMT1 methylation. Depletion of AKT1 or overexpression of dominant-negative AKT1 increases methylated DNMT1, resulting in a decrease in DNMT1 abundance. In mammalian cells, phosphorylated DNMT1 is more stable than methylated DNMT1. These results reveal cross-talk on DNMT1, through modifications mediated by AKT1 and SET7, that affects cellular DNMT1 levels.Multiple interdependent post-translational modifications of cellular proteins allow for combinatorial repertoires of interactions. Some of these modifications, including acetylation, phosphorylation, methylation and sumoylation, might participate in cross-talk for dynamic control of cellular signaling under various physiological conditions 1 . Protein phosphorylation is involved in various cellular processes, including cell growth, development and apoptosis, and regulates essential physiological systems, such as the period of the circadian rhythm within mammalian cells, via cellular signaling pathways 2 . Protein methylation, especially on lysines, is another important reversible post-translational modification of cellular proteins; for example, histone methylation is involved in the © 2011 Nature America, Inc. All rights reserved.Correspondence should be addressed to S.P. (pradhan@neb.com). Accession codes. Protein Data Bank: The coordinates and structure factors of the SET7-DNMT1 peptide complex have been deposited with accession code 3OS5.Note: Supplementary information is available on the Nature Structural & Molecular Biology website.AUTHOR CONT RIBUTIONS P.-O.E. performed cell biology and biochemistry experiments. M.S. made constructs, tested kinetics and performed the pull-down assay. G.R.F. performed quantitative PCR. Y.C. performed SET7 purifications, MS-based methylation assays on DNMT1 peptide, mutagenesis of K142R and crystallization of SET7-DNMT1 peptide. A.K.U. purified the DNMT1 N-terminal domain and performed MS-based methylation assays on this fragment. J.R.H. performed crystallographic experiments. X.C. and S.P. organized and analyzed data and wrote the manuscript. COMPETING FINANCIAL INT ERESTSThe authors declare no competing financial interests.Reprints and permissions information is available online at http://npg.nature.com/reprintsandpermissions/. Previously, we have demonstrated that methylation of Lys142 on DNMT1 leads to DNMT1 degradation15. Adjacent to Lys142 is Ser143, a known phosphorylation site 16 . Therefore, we s...

DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8–11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.

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