The Human Proteins MBD5 and MBD6 Associate with Heterochromatin but They Do Not Bind Methylated DNA

Abstract

BackgroundMBD5 and MBD6 are two uncharacterized mammalian proteins that contain a putative Methyl-Binding Domain (MBD). In the proteins MBD1, MBD2, MBD4, and MeCP2, this domain allows the specific recognition of DNA containing methylated cytosine; as a consequence, the proteins serve as interpreters of DNA methylation, an essential epigenetic mark. It is unknown whether MBD5 or MBD6 also bind methylated DNA; this question has interest for basic research, but also practical consequences for human health, as MBD5 deletions are the likely cause of certain cases of mental retardation.Principal FindingsHere we report the first functional characterization of MBD5 and MBD6. We have observed that the proteins colocalize with heterochromatin in cultured cells, and that this localization requires the integrity of their MBD. However, heterochromatic localization is maintained in cells with severely decreased levels of DNA methylation. In vitro, neither MBD5 nor MBD6 binds any of the methylated sequences DNA that were tested.ConclusionsOur data suggest that MBD5 and MBD6 are unlikely to be methyl-binding proteins, yet they may contribute to the formation or function of heterochromatin. One isoform of MBD5 is highly expressed in oocytes, which suggests a possible role in epigenetic reprogramming after fertilization.

Clinical and Molecular Aspects of MBD5-Associated Neurodevelopmental Disorder (MAND)

“…2 Structure of the MBD5 gene MBD5 has two known isoforms, 1 (UniProtKB ID # Q9P267-1) and 2 (UniProtKB ID # Q9P267-2). 18 Isoform 1 is the longer primary isoform and has 1448 amino acids encoded by exons 6-15 ( Figure 3a). 18 The protein has two conserved domains, a MBD and a proline-tryptophan-tryptophan-proline (PWWP) domain, both of which may be found in chromatin-associated proteins (Figure 3b).…”

“…18 Isoform 1 is the longer primary isoform and has 1448 amino acids encoded by exons 6-15 ( Figure 3a). 18 The protein has two conserved domains, a MBD and a proline-tryptophan-tryptophan-proline (PWWP) domain, both of which may be found in chromatin-associated proteins (Figure 3b). Isoform 2 is encoded by exons 6-9, with intron 9 being retained (Figure 3c), resulting in a protein of 851 amino acids that does not contain the PWWP domain (Figure 3d).…”

Basic concepts of epigenetics

“…45,[74][75][76] MBD5 is unique in that it harbors a secondary proline-tryptophan-tryptophan-proline domain, which can allow direct docking to chromatin, and is generally concentrated in areas with DNMT3a/3b, suggesting a role in newly established patterned heterochromatin. 71 All of these studies clearly show the importance of MBD proteins in bringing together methylated CpGs and reinforcements that ultimately model and shape the histone scaffold to constrict around methylated areas of DNA targeted for silencing.…”

“…These include: (1) BAZ2A/TIP5 and BAZ2B; (2) KMT1F/CLLD8, KMT1E/SETDB1 and (3) KIAA1461/MBD5 and KIAA1887/MBD6. 45,71 Little is known about the function of BAZ2B. There is evidence to suggest that it can dock to methylated DNA through its primary MBD domain, also having a secondary DNA-binding homeobox and different transcription factor domain, a tertiary tandem C4HC3 zinc-fingerlike domain and a quaternary AT hook domain, which is capable of binding to DNA, also being part of the N-CoR complex.…”

Epigenetic Regulation of Aldosterone Synthase Gene by Sodium and Angiotensin II

“…DNA methylation is associated with the formation of heterochromatin and gene silencing. The methyl‐CpG binding domain (MBD) proteins are capable of directly binding to methylated DNA 5, 6. Methyl‐CpG binding protein 2 (MECP2), MBD1, and MBD2 can repress methylation‐based transcription 7.…”