Methyl-CpG Binding Domain 1 (MBD1) Interacts with the Suv39h1-HP1 Heterochromatic Complex for DNA Methylation-based Transcriptional Repression

Abstract

DNA and protein modifications create a new surface for interaction with target molecules (1-5). Cytosine methylation is involved in gene regulation and the formation of transcriptionally inactive chromatin, together with methyl-CpG binding domain proteins (MBD 1 proteins) (6 -7). There are at least five mammalian MBD proteins, namely MeCP2, MBD1, MBD2, and MBD3 for transcriptional repression, and MBD4 (also known as MED1) for mismatch repair as a thymine glycosylase. In addition, posttranslational modifications of amino termini of the core histones cooperatively produce epigenetic codes for genome dynamics in the nucleus. These include acetylation, phosphorylation, and methylation of the histone molecules.Recent studies of cytosine hypomethylation mutants have revealed that both DNA methylation and histone modifications share a common pathway in chromatin organization (8). The Neurospora crassa DIM-5 gene product is a histone H3 methylase containing a SET domain, which specifically methylates lysine 9 of histone H3, abbreviated throughout as H3 (Lys-9). The mutant dim-5 completely abolished cytosine methylation of the genome. Furthermore, Arabidopsis thaliana DDM1, which shows amino acid similarity to a helicase of the SWI2/ SNF2 family, is also required for the maintenance of genomic methylation (9), and disruption of the homolog Lsh gene caused demethylation of the mouse genome (10). These suggest that DNA methylation may depend on methyl-H3 (Lys-9) and unique chromatin structure. However, interrelations between cytosine methylation, MBD proteins, and the histone-modifying system remain to be elucidated (1,3,11).MBD1 is known to act as a transcriptional repressor through the cooperation of MBD, cysteine-rich CXXC domains, and a C-terminal transcriptional repression domain (TRD) (12-15). The conserved CXXC sequence was originally found in DNMT1 and the trithorax group protein ALL-1, but its precise role is unknown (12, 15). MBD1 produces an active transcriptional repression that was partially reversed by the addition of histone deacetylase inhibitors (13). During investigation of the mechanism of transcriptional repression by the TRD of MBD1, we have recently found that a transcriptional mediator, MBD1-containing chromatin associated factor (MCAF), binds the TRD of MBD1 to form the repressive complex (16). In addition, the MBD of MBD1 binds a symmetrically methylated CpG sequence (17), but transcriptional roles of this domain have not been investigated. Little is understood about the state of histone modifications within MBD1-containing heterochromatin on methylated gene promoters. In this study, we show that H3 (Lys-9) methylase Suv39h1 and the methyl lysine-binding protein HP1 interact with MBD of MBD1. Suv39h1 enhances MBD1-mediated transcriptional repression via MBD but not the C-terminal TRD of MBD1. Furthermore, MBD1 associates with histone deacetylases through Suv39h1. Our data suggest that MBD1 tethers the Suv39h1-HP1 complex to methylated DNA regions. We discuss the possible pathway from DNA

Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin

“…Obviously, very low transcriptional activity might have escaped detection. The recently discovered in vitro and in vivo interaction of human proteins recognizing methylated cytosine in CpG (MeCP2, MBD1) with histone methyltransferase also suggests such a link (31,32). The effect of CpG methylation loss in the met1 is in contrast to methylation outside CpGs, which has no effect on H3K9 Me when strongly reduced by cmt3 (chromomethylase 3) mutations (12,33).…”

DNA methylation and the formation of heterochromatin in Neurospora crassa

“…Thus, HP1 provides the link between H3K9me3 established by DIM-5 and DNA methylation established by DIM-2 (Figure 1). Although these studies of HP1 in Neurospora have provided a direct link between HP1 and DNA methyaltion, HP1 proteins have also been shown to interact and/or colocalize with DMTs and methyl-binding proteins in mammals (Bachman et al, 2001;Fujita et al, 2003;Fuks et al, 2003;Reese et al, 2003). On the other hand, the Arabidopsis HP1 homologue, TFL2/LHP1, is dispensable for DNA methylation (Malagnac et al, 2002).…”

Epigenetic Information and Estrogen Receptor Alpha Expression in Breast Cancer

“…Subsequently, several MBD proteins have been identified that, similar to MeCP2, couple methylated DNA to HDAC [28,29]. The recruitment of MeCP2 to methylated CpG dinucleotides represents a major mechanism by which DNA methylation can repress transcription [30,31].…”