Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

Abstract

DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymethylation. Here we discuss the distinct landscape of DNA methylation in neurons, how it is established, and how it might affect the binding and function of protein readers of DNA methylation. We review studies of one critical reader of DNA methylation in the brain, the Rett syndrome protein methyl CpG-binding protein 2 (MeCP2), and discuss how differential binding affinity of MeCP2 for non-CpG and hydroxymethylation may affect the function of this methyl-binding protein in the nervous system.M ethylation of cytosines at the carbon 5 position (5-methylcytosine, mC) constitutes the most common covalent modification of vertebrate genomic DNA. Traditionally, cytosine methylation in vertebrate genomes has been viewed as largely restricted to CpG dinucleotide (CG) sequences, providing a stable epigenetic mark that mediates long-term transcriptional silencing. Indeed, 60-90% of all CGs are methylated in mammalian genomes, and CG methylation (mCG) has been shown to play critical roles in genomic imprinting, X-chromosome inactivation, cellular differentiation, and development (1). In addition, the disruption of cellular DNA methylation patterns has been linked to human disease, including multiple cancers (2, 3).Evidence that DNA methylation has a uniquely important role in the brain emerged almost two decades ago with the discovery of the prominent methyl-DNA-binding protein, methyl-CpG-binding protein 2 (MeCP2), and the later identification that mutations in MeCP2 give rise to the X-linked neurological disorder Rett syndrome (RTT) (4-6). Subsequent studies also have identified neurodevelopmental disorders associated with mutations in DNA methyltransferases (7), suggesting that both the enzymatic "writers" of DNA methylation patterns and the "readers" of these marks have important roles in the brain. In this context, new studies from several laboratories have uncovered extensive cytosine modification in the brain beyond mCG. Non-CG methylation (CH methylation or mCH, in which H = A, C, or T) is now appreciated to accumulate in the human and mouse brain postnatally, reaching levels similar to that of mCG in the neuronal genome (8, 9). Moreover, oxidation of mC by the ten-eleven translocation (Tet) family of dioxygenases leads to the selective accumulation of 5-hydroxymethylcytosine (hmC) in the adult brain, together with its more highly oxidized derivatives 5-formylcytosine and 5-carboxylcytosine (10, 11). This finding suggests that hmC may act as an intermediate in an active DNA demethylation pathway, though growing evidence also suggests that hmC may serve as a stable neuronal epigenetic mark in its own right (12).The discovery of these previously unidentified brain-enriched forms of DNA methylation provides...

Analysis of DNA modifications in aging research

“…e CG methylation is typically low over CG islands but higher in shores and shelves. f CG methylation across promoters often varies greatly across a relatively narrow region with lowest methylation typically observed around the transcription start site (TSS), even in un-expressed genes CH sites and hydroxymethylation of CG sites are prevalent in several organ systems, particularly the central nervous system (Lister et al 2013;Kinde et al 2015). The high levels of hmCG and mCH in the brain stand in contrast to other organs (Nestor et al 2012) and suggest the possibility that the epigenomics of the aging brain is substantially different from other tissues (Masser et al 2017a).…”

“…Within gene bodies, both mCG and hmCH are positively associated with gene expression (Lister et al 2013;Lou et al 2014). Promoter mCH is inversely correlated to gene expression and gene body mCH varies in its relationship to gene expression, being either repressive or associated with increased expression (Lister et al 2013;Kinde et al 2015;Lister and Mukamel 2015). The relationship of hmCH to gene expression is unknown, although it does appear that hmCH levels are extremely low (Hadad et al 2016).…”

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

“…Methods that fail to assay each strand cannot comprehensively quantify non-CG methylation, which is asymmetric and an emerging element of epigenetic regulation of gene expression (Kinde et al 2015). Additionally, strand-specific RNA sequencing is becoming the gold standard for transcript expression analysis; therefore, integrating strand-specific data sets of DNA methylation and RNA expression has the potential to yield greater insights into transcript regulatory processes over conventional strand-independent methods.…”

Exaggerated CpH Methylation in the Autism-Affected Brain

“…http://dx.doi.org/10.1101/069120 doi: bioRxiv preprint first posted online Aug. 11, 2016; ultimately reaching levels similar to that of CpG methylation (mCG) in brain DNA [13][14][15] . In contrast to mCG, which remains largely unchanged during postnatal development, mCH accumulation correlates with synaptogenesis and increases especially during the first few years of life 13,14 , a time period of particular interest in autism.…”