Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis

H3K36me3 (ChIp-ChIp), H3K4me3 (ChIp-ChIp), H3K27me3 (ChIp-ChIp), 5mC (MIRA) and 5hmC (hMeDIP) profiles were analyzed in neural progenitor cells (NPC) and neurons by using Nimblegen Mouse ChIP-chip 2.1M Economy Whole-Genome Tiling - 4 Array Set. In order to compare two different techniques of 5hmC profiling, we performed 5hmC profiling with Hydroxymethyl Collector™ Kit (Active Motif) method and hybridized it on mouse Chr7 fragment (Nimblegen). As an independent experiment, 5hmC profiling was performed by using hMeDIP method and hybridized on mouse Chr7 fragment (Nimblegen). After MIRA enrichment and genome amplification, DNA was hybridized on mouse Chr7 fragment (Nimblegen). Analysis of epigenetic changes during neural differentiation due to comparisson of epigenetic patterns in neural progenitor cells versus neurons.

本研究采用Nimblegen小鼠ChIP-chip 2.1M Economy全基因组平铺阵列-4套装，对神经祖细胞（neural progenitor cells, NPC）及神经元中的H3K36me3 (ChIp-ChIp)、H3K4me3 (ChIp-ChIp)、H3K27me3 (ChIp-ChIp)、5mC (MIRA)及5hmC (hMeDIP)谱进行了分析。为对比两种不同的5hmC谱检测技术，我们使用Hydroxymethyl Collector™ Kit (Active Motif)试剂盒完成5hmC谱检测，并将其杂交至小鼠7号染色体片段阵列（Nimblegen）。作为独立实验，我们还采用hMeDIP方法开展5hmC谱检测，并将其杂交至小鼠7号染色体片段阵列（Nimblegen）。经MIRA富集与基因组扩增后，将DNA样本杂交至小鼠7号染色体片段阵列（Nimblegen）。本研究通过对比神经祖细胞与神经元的表观遗传谱模式，分析神经分化过程中的表观遗传变化。