Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
Department of Systems Pharmacology and Translational Therapeutics and Penn Epigenetics Institute, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
J Neurosci Methods. 2018 Oct 1;308:62-73. doi: 10.1016/j.jneumeth.2018.07.006. Epub 2018 Jul 18.
High-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.
Single 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.
ChIP-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.
S3EQ 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.
The S3EQ method can be applied to improve the correlative power of transcriptomic and epigenomic studies in neuronal tissue.
高通量测序技术已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的神经功能中的作用。然而，现有的数据受到以下事实的限制：只有在单独的队列中测量了表观遗传和转录组变化。这限制了对基因表达中表观遗传变化的精确相关性。
单样本测序（S3EQ）是一种分析单个神经元样本中表观遗传和转录组调控的创新方法。使用这种方法，我们分析了来自相同动物伏隔核（NAc）的染色质免疫沉淀（ChIP）和 RNA 测序数据。
神经元核内的 ChIP-S3EQ 可靠地鉴定了成年小鼠 NAc 中的 hPTM 富集，具有很高的精度。通过比较细胞区室，我们发现全细胞 RNA-seq 的剪接体比核 RNA-seq 更能被细胞质 RNA-S3EQ 更好地再现。最后，S3EQ 显示出更高的灵敏度来关联染色质修饰与基因表达，尤其是对于低表达的转录物。
S3EQ 能够从单个样本中准确地生成 RNA 和 ChIP-seq，这明显优于需要两个样本的现有方法。ChIP-S3EQ 的性能与 ChIP-seq 相当，而 RNA-S3EQ 生成的表达谱几乎与核富集和全细胞 RNA-seq 相同。最后，我们直接比较了细胞区室的 RNA-seq，解决了仅限于神经元核的 RNA-seq 研究的局限性。
S3EQ 方法可用于提高神经组织中转录组和表观基因组研究的相关性。
