Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods.
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods.
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DOI：
10.3390/genes13020306
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发表时间：
2022-02-06
期刊：
影响因子：
3.5
通讯作者：
Feng J
中科院分区：
文献类型：
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作者：
Li Y;Xu H;Chitaman JM;Feng J
DNA甲基化在各种细胞过程中起着重要作用。下一代测序使我们能够研究整个基因组中DNA甲基化的功能意义。然而，这种方法通常需要大量的基因组DNA，这限制了其应用于离散脑区域内的定义的细胞类型。在这里，我们应用了两种不同的方案，AM-Seq和EM-Seq，来分析小鼠延髓核（NAc）中表达D2多巴胺受体的中型多刺神经元（D2-MSN）的甲基化组。使用从FACS分离的D2-MSNs提取的40 ng DNA，我们发现两种方法都产生了高质量的甲基化组数据。此外，我们确定了许多未甲基化区域（UMR）作为细胞类型特异性调控区。通过比较NAc D2-MSN甲基化组与已发表的小鼠前额叶皮层兴奋性神经元和神经祖细胞（NPC）的甲基化组，我们鉴定了许多差异甲基化的CpG和非CpG区域。我们的研究不仅提供了这两种低输入DNA全基因组甲基化分析方案的比较，而且还提供了小鼠脑D2-MSNs的DNA甲基化组的资源，这是一种在成瘾和其他神经精神疾病中起关键作用的神经元类型。
DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders.
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影响因子：
14.9
作者：
Feng H;Conneely KN;Wu H
通讯作者：
Wu H
影响因子：
14.9
作者：
Burger L;Gaidatzis D;Schübeler D;Stadler MB
通讯作者：
Stadler MB
DOI：
10.1073/pnas.1505909112
发表时间：
2015-04-28
影响因子：
11.1
作者：
Chen, Lin;Chen, Kaifu;Zoghbi, Huda Y.
通讯作者：
Zoghbi, Huda Y.
影响因子：
12.3
作者：
Feng J;Wilkinson M;Liu X;Purushothaman I;Ferguson D;Vialou V;Maze I;Shao N;Kennedy P;Koo J;Dias C;Laitman B;Stockman V;LaPlant Q;Cahill ME;Nestler EJ;Shen L
通讯作者：
Shen L
影响因子：
46.9
作者：
通讯作者：
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