Injury-induced DNA methylome plasticity in the peripheral nervous system of the rat [article]

Meike Gölzenleuchter, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2015
Recently, the dynamic characteristics of the adult methylome have been demonstrated in the central nervous system. Whether external stimuli can provoke DNA methylation changes in the peripheral nervous system has not been studied. The present work was based on the hypothesis that L5 spinal nerve injury induces DNA methylation changes in the L5 rat dorsal root ganglion (DRG). A rodent model of neuropathic pain, the Spinal Nerve Ligation (SNL) was employed to test this hypothesis. Methods:
more » ... representation bisulfite sequencing (RRBS) was used to analyze DNA methylation of eight rat DRGs (four controls, four SNL). This method makes it possible to profile DNA methylation on a genome-wide scale, at single-nucleotide resolution. First, DNA is digested with a methylation-insensitive restriction enzyme, yielding fragments that contain at least two cytosine-phosphate-guanine-dinucleotides (CpGs). Subsequently the fragments are bisulfite-treated, leading to the desamination of the unmethylated cytosines into uracils, without affecting the other bases. Finally the fragments are amplified, sequenced and aligned to the reference genome. Results: Using an early time point of 24h post ligation this work reports widespread, highly significant (p≤10-4) cytosine hyper- and hypomethylation in about 1% of the 1.4 million CpGs captured by RRBS. These CpGs were termed dynamically differentially methylated CpGs (dDMCs). The epigenetic remodeling occurred mainly outside of CpG islands. 56% of the observed changes were located in promoter or genic regions and mainly affected genes belonging to the axon guidance pathway (p<10-11). Consistent with emerging models relying on genome-wide methylation and RNA-sequencing analysis, variation of methylation was not tightly linked with variation of gene expression. 44% of the dynamically changed CpGs were detected outside of genes. These intergenic dDMCs occurred in clusters, with neighboring dDMCs varying in the same direction. The positions of these dDMCs were compared to [...]
doi:10.17169/refubium-5954 fatcat:6ciymn6xubbxlkfnwyp253o5j4