Methylation specific targeting of a chromatin remodeling complex from sponges to humans

Abstract

DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.

Structural Basis of MeCP2 Distribution on Non-CpG Methylated and Hydroxymethylated DNA

“…For comparison, we assessed mCA recognition by MBD2, which shows very high selectivity for mCG [16,24] and represents the most evolutionarily ancient MBD protein [25,26] (Fig. 3A).…”

“…The residue-specific changes in the amide backbone of MeCP2 bound to the BDNF promoter sequences were monitored by 1 H/ 15 N-Heteronuclear Single-Quantum Correlation (HSQC) NMR spectroscopy and compared using standard chemical shift perturbations (CSPs). In NMR studies of the MBD family proteins, we identified linear chemical shift changes that correlate with methylated DNA binding and present in every ortholog and paralog examined to date [13,26–28]. In particular, two of these resonances (Gly 27 and Ala 30 of MBD2) show large CSPs between the non-specific and methylation-specific binding modes, such that we have used these resonances as reporters of mCG binding [27].…”

DNA Methylation Changes in Human Papillomavirus-Driven Head and Neck Cancers

“…These factors, when bound to methylated DNA, are capable of restricting the access for transcription factors causing downregulation of the gene expression [38]. Furthermore, members of MBD family proteins are capable of interacting with histone modification enzymes, promoting a more closed chromatin structure in order to restrict the access for the transcription machinery [39,40].…”

Wnt signaling and polarity in freshwater sponges

“…A 28% knockdown of EmuGSK-3 for this experiment was confirmed with two internal replicates by qPCR, using EmuEf1-α as the housekeeping reference gene (Additional file 9 ). Though the RNAi technique as currently used in E. muelleri only results in knockdown of ~30% (range of ~20–50% depending on the gene tested), phenotypes of EmuGSK-3 knockdown sponges were distinct from those observed in other knockdown experiments targeting different genes [ 25 – 27 ].…”