An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex.

Megha A Desai,Leander M Sinanan,J Neel Scarsdale,Ninad M Walavalkar,Heather D Webb,Gordon D Ginder,David C Williams

doi:10.1093/nar/gkv168

Megha A Desai, Leander M Sinanan + Show 5 more

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https://doi.org/10.1093/nar/gkv168

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Abstract

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.

Highlights

Epigenetic regulation comprises heritable changes in gene expression most commonly brought about by DNA methylation and histone modifications
We show that this region is intrinsically disordered in isolation and in the context of the full-length protein bound to DNA, we identify its role in modifying kinetics and affinity of DNA-binding, and map the critical sites needed for MBD2IDR to recruit the histone deacetylase core complex within the context of the intact MBD2 protein in cells
The 1H-15N⑀ resonances of two Trp residues completely overlap, while seven Asn and ten Gln sidechain 15N1H2 resonances overlap extensively. These findings indicate that the MBD2IDR domain remains largely disordered in solution

Summary

Introduction

Epigenetic regulation comprises heritable changes in gene expression most commonly brought about by DNA methylation and histone modifications. Regions of high CpG density are often associated with gene promoters [2], which remain unmethylated except for a subset of tissue-specific genes involved in normal differentiation and development [3,4,5,6]. Aberrant hypermethylation of tumor suppressor gene promoters is associated with oncogenesis in a wide array of tissues [7]. The methyl-CpG binding domain (MBD) family proteins recognize this methylated mark and repress the associated genes by recruiting different co-repressor complexes. With the exception of mammalian MBD3, all MBD proteins bind to methylated DNA with varying affinities [10,11,12,13]

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