Brain neuronal cell nuclei with exceptionally high levels of hydroxymethylcytosine

We recently reported that a significant subpopulation of adult mouse brain cellular nuclei (NeuN-High) have highly decondensed chromatin characteristic of multipotent cells types (Yu et al., DNEU, 2015). Herein we show that NeuN-High nuclei also have significantly higher levels of 5´-hydroxymethylcytosine (5hmC), a rate limiting intermediate in the turnover of modified cytosine. TET-assisted bisulfite sequencing demonstrated that 5hmC levels in NeuN-High nuclei spiked rapidly from 20% to nearly 40% of CG dinucleotides at the start of gene regions for various classes of the most highly transcribed neuron-specific genes, but were variably distributed among different functional gene categories and in well-defined gene regions. NeuN-Low neuronal and non-nueronal neuronal nuclei had significantly lower levels of 5hmC for all classes of expressed genes. In summary, these data support the view that an elevated turnover rate for chromatin modifications may potentiate the cellular memory of the most active subclasses of neurons. TAB-seq data was collected from genomic DNA isolated from NeuN-High, NeuN-Low and NeuN-Neg Mus musculus brain cell nuclei.