Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens.
Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens.
复制标题
伏隔核表观基因组和转录组的单样本测序 (S3EQ)。
DOI：
10.1016/j.jneumeth.2018.07.006
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发表时间：
2018
影响因子：
3
通讯作者：
Heller,EA
中科院分区：
文献类型：
--
作者：
Xu,SJ;Heller,EA
背景高通量测序已被广泛应用于揭示神经和精神疾病的分子机制。大量数据支持表观遗传机制在人类和动物神经功能中的作用。然而，现有的数据受到这样一个事实的限制，即表观遗传和转录变化只在不同的队列中进行了测量。这限制了基因表达的表观遗传变化的精确相关性。新方法单一样本测序(S3EQ)是一种创新的方法，可以分析单个神经元样本中的表观遗传和转录调控。结果神经元核团ChIP-S3EQ能准确、可靠地鉴定成年小鼠伏隔核中hPTM的表达。比较细胞间隔室，我们发现胞质RNA-S3EQ比核RNA-SEQ更紧密地重排了整个细胞RNA-seq的剪接体。与现有的方法相比，S3EQ能够准确地从单个样本中同时生成RNA和ChIP-SEQ，与需要两个样本的现有方法相比，S3EQ具有明显的优势。CHIP-S3EQ的性能与CHIP-SEQ相当，而RNA-S3EQ产生的表达谱与核富集型和全细胞RNA-SEQ几乎相同。结论S3EQ方法可用于提高神经元组织转录与表观基因组学研究的相关性。
BackgroundHigh-throughput sequencing has been widely applied to uncover the molecular mechanisms underlying neurological and psychiatric disorders. The large body of data support the role of epigenetic mechanisms in neurological function of both human and animals. Yet, the existing data is limited by the fact that epigenetic and transcriptomic changes have only been measured in separate cohorts. This has limited precise correlation of epigenetic changes in gene expression.New methodSingle Sample Sequencing (S3EQ) is an innovative approach to analyze both epigenetic and transcriptomic regulation within a single neuronal sample. Using this method, we analyzed chromatin immunoprecipitation (ChIP)- and RNA-sequencing data from the nucleus accumbens (NAc) of the same animal.ResultsChIP-S3EQ of neuronal nuclei reliably identified hPTM enrichment in the adult mouse NAc with high precision. Comparing cellular compartments, we found that the spliceosome of whole cell RNA-seq was more closely recapitulated by cytosolic RNA-S3EQ than nuclear RNA-seq. Finally, S3EQ showed increased sensitivity for correlating chromatin modifications with gene expression, especially for lowly expressed transcripts.Comparison with existing methodsS3EQ accurately generates both RNA- and ChIP-seq from a single sample, providing a clear advantage over existing methods which require two samples. ChIP-S3EQ performance was comparable to ChIP-seq, while RNA-S3EQ generated an almost identical expression profile to nuclear-enriched and whole cell RNA-seq. Finally, we directly compared RNA-seq by cellular compartments, addressing a limitation of RNA-seq studies limited to neuronal nuclei.ConclusionThe S3EQ method can be applied to improve the correlative power of transcriptomic and epigenomic studies in neuronal tissue.