Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

Abstract

SUMMARY DNA methylation in mammals is highly dynamic during germ cell and pre-implantation development but is relatively static during development of somatic tissues. 5-hydroxymethylcytosine (5hmC), created by oxidation of 5-methylcytosine (5mC) by Tet proteins and most abundant in brain, is thought to be an intermediate towards 5mC demethylation. We investigated patterns of 5mC and 5hmC during neurogenesis in the embryonic mouse brain. 5hmC levels increase during neuronal differentiation. In neuronal cells, 5hmC is not enriched at enhancers but associates preferentially with gene bodies of activated neuronal function-related genes. Within these genes, gain of 5hmC is often accompanied by loss of H3K27me3. Enrichment of 5hmC is not associated with substantial DNA demethylation suggesting that 5hmC is a stable epigenetic mark. Functional perturbation of the H3K27 methyltransferase Ezh2 or of Tet2 and Tet3 leads to defects in neuronal differentiation suggesting that formation of 5hmC and loss of H3K27me3 cooperate to promote brain development.

SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis

“…During development, TrxG and PcG complexes at bivalent domains play a key role in fine-tuning the expression of genes encoding crucial factors and in defending against unscheduled gene activation (57). Differentiation of neural progenitors is accompanied by an epigenetic switch characterized by a decrease of H3K27me3 and a gain of H3K4me3 at the promoters of proneural genes (6). Exogenous SOX2 expression previously was shown to be sufficient to reprogram fibroblasts into multipotent neural stem cells (NSCs) (55) or, in combination with Mash1, to reprogram human brain pericytes into neuronal cells (58).…”

“…In NPCs, the chromatin regions of proneural and neurogenic genes contain high levels of both H3K27me3 and H3K4me3 (37,38); such bivalent marks maintain the genes transcriptionally silent but poised for activation once differentiation cues are received (32). To understand the regulatory function of SOX2 in activation of the neurogenic program, we examined previously published ChIP-sequencing (ChIP-seq) data including the occurrence of H3K27me3 and H3K4me3 marks at SOX2-binding sites in mouse ES cell-derived NPCs (6,26). Genomewide analysis revealed that of the 16,683 SOX2-binding sites, 2,514 were enriched for H3K27me3 (15.1%) (Fig.…”

“…Recent genomewide analyses of epigenetic regulators in the brain have provided considerable insight into the mechanisms that regulate neural development, neurological disease, and aging (4,5). The chromatin states of NPCs change dynamically during cell-fate determination and cell differentiation, and chromatin marks such as histone H3 trimethylated Lys 27 (H3K27me3), histone H3 trimethylated Lys 4 (H3K4me3), and histone H3 acetylated Lys 9 (H3K9ac) are essential for regulating the expression of key genes involved in these processes (6). Sex-determining region Y (SRY)-related HMG box 2 (SOX2) is a member of the SOXB1 family of transcription factors, which play important roles in maintaining neural stem/progenitor cell properties, including their capacity to proliferate and self-renew (7,8).…”

Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation

“…1A). Hydroxymethylation of cytosines has been suggested to play an important role in neurons due to the abundance of this mark in the brain (Hahn et al 2013;Rudenko et al 2013). Therefore, we hypothesized that this epigenetic mark might also be critical for the proliferation and/or differentiation of intestinal epithelial cells.…”

Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

“…5-hmC is highly enriched in the adult brain (7), dynamically regulated by neural activity (8), and accumulates across the lifespan (9). This epigenetic mark is critically involved in neuronal differentiation and in the reprogramming of pluripotent stem cells (10), and rather than being an intermediate state of active DNA demethylation, 5-hmC can be either dynamic or stable (8,10). Unlike its repressive cousin, 5-mC, which is primarily found along CpG-rich gene promoters, 5-hmC is enriched within gene bodies and at intronexon boundaries of synaptic plasticity-related genes, as well as within distal cis-regulatory elements, which together point to an important role for 5-hmC in coordinating transcriptional activity (11)(12)(13).…”