Nucleosome remodeling complexes comprise several large families of chromatin modifiers that integrate multiple epigenetic control signals to play key roles in cell type-specific transcription regulation. We previously isolated a methyl-binding domain protein 2 (MBD2)-containing nucleosome remodeling and deacetylation (NuRD) complex from primary erythroid cells and showed that MBD2 contributes to DNA methylation-dependent embryonic and fetal β-type globin gene silencing during development in vivo. Here we present structural and biophysical details of the coiledcoil interaction between MBD2 and p66α, a critical component of the MBD2-NuRD complex. We show that enforced expression of the isolated p66α coiled-coil domain relieves MBD2-mediated globin gene silencing and that the expressed peptide interacts only with a subset of components of the MBD2-NuRD complex that does not include native p66α or Mi-2. These results demonstrate the central importance of the coiled-coil interaction and suggest that MBD2-dependent DNA methylation-driven gene silencing can be disrupted by selectively targeting this coiled-coil complex.epigenetics | gene regulation D NA methylation involves the enzymatic addition of a methyl group at the C5 position of symmetrically opposed cytosine bases in a double-stranded cytosine-guanosine sequence (CpG). Regions of increased CpG content (CpG islands) often are found associated with promoters and, when methylated, silence expression of the associated gene (1, 2). Although most CpG islands are largely unmethylated in normal adult tissues, a subset of CpG islands is methylated in specific tissue subtypes, stages of differentiation, and development. Importantly, hypermethylation and silencing of tumor suppressor genes represents a pro-oncogenic change found in a wide range of malignancies (3). These observations have raised interest in DNA methylation as both an important genetic regulatory mechanism and a potential therapeutic target for either re-expression of developmentally silenced genes or reversing tumor suppressor gene silencing in cancer (4, 5).The methyl cytosine binding proteins include a family that specifically recognizes the methylated CpG sequence through an ∼60 amino acid methyl-binding domain (MBD). There are five members of the MBD family in mammals: methyl CpG-binding protein 2 (MeCP2), the first to be identified (6), and MBD1 through MBD4 (7). We and others have isolated and characterized an MBD2-containing nucleosome remodeling and deacetylation (NuRD) complex (referred to as "MBD2-NuRD") that binds methylated DNA and regulates transcription of the associated gene (8-10). The MBD2-NuRD complex comprises at least one homolog of six core proteins: MBD2, retinoblastoma protein-associated protein (RbAp46 or -48) Mi-2(α or β), p66(α or β), histone deacetylase (HDAC1 or 2), and metastasis associated (MTA1 or -2) (Fig. 1A). However, the specific interactions involved in the formation of the MBD2-NuRD complex have not been delineated clearly; information that is key to understanding (i) ...

The MBD2-NuRD (Nucleosome Remodeling and Deacetylase) complex is an epigenetic reader of DNA methylation that regulates genes involved in normal development and neoplastic diseases. To delineate the architecture and functional interactions of the MBD2-NuRD complex, we previously solved the structures of MBD2 bound to methylated DNA and a coiled-coil interaction between MBD2 and p66α that recruits the CHD4 nucleosome remodeling protein to the complex. The work presented here identifies novel structural and functional features of a previously uncharacterized domain of MBD2 (MBD2IDR). Biophysical analyses show that the MBD2IDR is an intrinsically disordered region (IDR). However, despite this inherent disorder, MBD2IDR increases the overall binding affinity of MBD2 for methylated DNA. MBD2IDR also recruits the histone deacetylase core components (RbAp48, HDAC2 and MTA2) of NuRD through a critical contact region requiring two contiguous amino acid residues, Arg286 and Leu287. Mutating these residues abrogates interaction of MBD2 with the histone deacetylase core and impairs the ability of MBD2 to repress the methylated tumor suppressor gene PRSS8 in MDA-MB-435 breast cancer cells. These findings expand our knowledge of the multi-dimensional interactions of the MBD2-NuRD complex that govern its function.

Background: Although highly homologous to MBD2, the functional role of MBD3 remains in question. Results: MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated CpG dinucleotides. Conclusion: Dynamic distribution between methylated and unmethylated sites modifies the genomic localization of MBD3. Significance: Changes in the dynamic distribution on DNA dictate functional differences between MBD proteins.

Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data. We show that seqOutBias correction facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.

Background:The MBD2-p66␣ coiled-coil interaction is key to the function of the NuRD chromatin remodeling complex. Results: Binding to p66␣ depends on helicity and electrostatic potential of the MBD2 domain. Conclusion: Variations in helical content and charge distribution dictate a binding affinity hierarchy for MBD2 homologues. Significance: Delineating determinants of binding will aid the development of inhibitors of these complexes.