5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes

Abstract

5-hydroxymethylcytosine (5hmC) occurs at maximal levels in postmitotic neurons, where its accumulation is cell-specific and correlated with gene expression. Here we demonstrate that the distribution of 5hmC in CG and non-CG dinucleotides is distinct and that it reflects the binding specificity and genome occupancy of methylcytosine binding protein 2 (MeCP2). In expressed gene bodies, accumulation of 5hmCG acts in opposition to 5mCG, resulting in “functional” demethylation and diminished MeCP2 binding, thus facilitating transcription. Non-CG hydroxymethylation occurs predominantly in CA dinucleotides (5hmCA) and it accumulates in regions flanking active enhancers. In these domains, oxidation of 5mCA to 5hmCA does not alter MeCP2 binding or expression of adjacent genes. We conclude that the role of 5-hydroxymethylcytosine in postmitotic neurons is to functionally demethylate expressed gene bodies while retaining the role of MeCP2 in chromatin organization.

MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions

“…Taken together, these data suggest that MeCP2 behavior in live neurons is tightly regulated by epigenetic modifications of the DNA. Thus, as predicted from previous biochemical studies Mellen et al, 2017), a decrease in the level of DNA methylation as a result of Dnmt3a deletion causes a reduction in the fraction of stably bound MeCP2 in vivo. Conversely an increase in DNA methylation as a consequence of deletion of the Tet oxidases results in an increase in the fraction of stably bound MeCP2.…”

“…Biochemical studies have initially determined that the ability of MeCP2 to bind DNA depends on the presence of methylated cytosines (5mC) and more recently, it was shown that hydroxylation of these sites (5hmC), when it occurs in the context of CpG, disrupts this interaction ( Figure 4SA) (Gabel et al, 2015;Mellen et al, 2017). Once neurons become postmitotic, they begin accumulating de novo DNA methylation sites by the activity of DNA methyltransferase 3a (DNMT3a), as well as converting 5mC to 5-hyroxymethylcytosine (5hmC) through the enzymes Tet1, 2 and 3 (Lister et al, 2013;Stroud et al, 2017).…”

“…Genome-wide mapping studies of MeCP2 have shown that it is enriched in highly methylated regions, although it can be found also in regions where levels of DNA methylation are low (Baubec et al, 2013;Mellen et al, 2017;Skene et al, 2010). Oddly, despite its high expression in neurons, MeCP2 is not sufficiently abundant to bind simultaneously to all methylated sites in the neuronal genome.…”

5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell

“…Similar to other tissue types, 5hmC is enriched in the bodies of actively transcribed genes in postmitotic neurons, and accumulates at the flanking region of enhancers and TF binding sites [15,85,86]. In addition, 5hmC was found to accumulate in adult neurons as synaptogenesis occurs, although its content and distribution varies among different kind of neurons [20].…”

“…Indeed, it was recently shown that distribution of 5hmC in CG and non-CpG dinucleotides is distinct and reflects the binding specificity and genome occupancy of MeCP2 [86]. In addition, loss of MeCP2 led to specific reduction of 5hmC signals in dynamically hydroxymethylated intragenic non-CpGs involved in gene activation [20].…”