Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication

Abstract

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.

Inhibition of Histone Methyltransferases SUV39H1 and G9a Leads to Neuroprotection in an in vitro Model of Cerebral Ischemia

“…9 Both SUV39H1 and G9a act in multiple repressive complexes and interact with regulatory elements to silence transcription. 12,13,29 The inhibition of these two histone methyltransferases can induce a shift from repressive to activating posttranslational histone modifications beyond H3 demethylation. Our observation that the knockdown of the transcriptional repressor G9a alone increases global H3K9 acetylation levels ( Figure 2A) -a sign for transcriptional derepression -is consistent with findings of others.…”

CXXC Domain of Human DNMT1 Is Essential for Enzymatic Activity

“…DNMT1 can also bind to unmethylated CpG DNA through its CXXC domain and thus induce transcriptional gene silencing in a DNA methylation independent manner. Once bound to unmethylated CpG DNA, DNMT1 can recruit histone H3 K9 methyltransferase G9a, to further lock chromatin into a repressed state (19). These modifications of chromatin that include histone deacetylation, methylation and DNA methylation make chromatin less accessible for transcription factors, which is observed during tumor suppressor gene repression in cancer cells.…”

“…Therefore, interaction and interplay between both regions is necessary for methyltransferase activity. The amino terminus region of the enzyme is also involved in methylation independent gene repression through recruitment of transcriptional repressors, such as retinoblastoma, histone deacetylase 1 (18), G9a (19), MeCP2 (20) and HP1 (21). These signature repressor elements could facilitate chromatin silencing in a cooperative manner.…”

Nucleosome assembly and epigenetic inheritance

“…CAF-1 is also reported to interact with chromatin factors, including MBD1 (methyl CpG-binding protein 1) and SETDB1 during heterochromatin DNA replication (Reese et al, 2003;Sarraf and Stancheva, 2004). In addition, DNMT1 directly interacts with histone H3K9 methyltransferase G9a, and recruits G9a to the replication foci (Estève et al, 2006). Using high resolution imaging techniques, Taddei et al (1999) provided evidences that CAF-1 persists on newly replicated DNA after its synthesis for a period of more than 20 min, in consistence with the in vitro finding that CAF-1 assembles nucleosome post-replication (Shibahara and Stillman, 1999).…”