Diversity of two forms of DNA methylation in the brain

Yuanyuan Chen,Feng C Zhou,Kenneth Dunn,Joseph Irudayaraj,Nur P Damayanti

doi:10.3389/fgene.2014.00046

Abstract

DNA methylation 5-methylcytosine (5mC) predicts a compacting chromatin inaccessible to transcription. The discovery of 5-hydroxymethylcytosine (5hmC), which is derived from 5mC, adds a new dimension to the mechanism and role of DNA methylation in epigenetics. Genomic evidence indicates that the 5hmC is located in the alternate regions to 5mC. However, the nature of 5hmC, as compared with classical 5mC remains unclear. Observing the mouse brain through embryonic development to the adult, first, we found that 5hmC is not merely an intermediate metabolite of demethylation, but is long lasting, chromatically distinct, and dynamically changing during neurodevelopment. Second, we found that 5hmC distinctly differs from 5mC in its chromatin affiliation during neural stem cell (NSC) development. Thirdly, we found both 5mC and 5hmC to be uniquely polarized and dynamic through the NSC development. 5mC was found to progressively polarize with MBD1 and MeCP2, and recruits H3K9me3 and H3K27me3; while 5hmC progressively co-localizes with MBD3 and recruits H3K4me2. Critical differential binding of 5mC with MBD1, and 5hmC with MBD3 was validated by Resonance Energy Transfer technique FLIM-FRET. This transition and polarization coincides with neuroprogenitor differentiation. Finally, at the time of synaptogenesis, 5mC gradually accumulates in the heterochromatin while 5hmC accumulates in the euchromatin, which is consistent with the co-localization of 5hmC with PolII, which mediates RNA transcription. Our data indicate that 5mC and 5hmC are diverse in their functional interactions with chromatin. This diversity is likely to contribute to the versatile epigenetic control of transcription mediating brain development and functional maintenance of adult brain.

Highlights

Since its discovery as the second form of DNA methylation in vertebrate tissue, 5-hydroxymethylcytosine (5hmC), which is most abundant in the brain (Globisch et al, 2010), has been in the eye of the epigenetic storm (Kriaucionis and Heintz, 2009; Tahiliani et al, 2009; Guo et al, 2011; Ito et al, 2011)
We demonstrated that 5mC dramatically increased in the neuroprogenitor cells during priming for differentiation, and preferentially binds to MBD1, and colocalizes with MeCP2, histone H3K9me3 and H3K27me3, and is packed into heterochromatin during and after neural differentiation. 5mC is likely to organize a more selective transcription during differentiation
5hmC surged at the initiation of differentiation of neuroepithelial cells, preferentially bound to MBD3, colocalized with the euchromatin histone H3K4me2, and gradually translocated to the euchromatin, demonstrating a transition to transcription that is needed for differentiation

Summary

Introduction

Since its discovery as the second form of DNA methylation in vertebrate tissue, 5-hydroxymethylcytosine (5hmC), which is most abundant in the brain (Globisch et al, 2010), has been in the eye of the epigenetic storm (Kriaucionis and Heintz, 2009; Tahiliani et al, 2009; Guo et al, 2011; Ito et al, 2011). The TET enzyme and the generation of 5hmC have been found to be involved in programming and maintenance of the pluripotency of embryonic stem (ES) cells (Ito et al, 2010) and totipotency of zygotes (Wossidlo et al, 2011). Recent genomic distribution analyses showed that 5hmC and 5mC are distributed in proximity to different categories of histone codes in the embryonic stem (ES) cells (Pastor et al, 2011; Stroud et al, 2011; Williams et al, 2011; Xu et al, 2011), which implicates the potential deviation of their action in ES cells

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