Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA.
Informatics Core, The Scripps Research Institute Jupiter, FL, USA.
Front Cell Neurosci. 2015 Mar 6;9:63. doi: 10.3389/fncel.2015.00063. eCollection 2015.
Despite the importance of the long non-coding RNAs (lncRNAs) in regulating biological functions, the expression profiles of lncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC), the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2759 lncRNAs and 17,859 mRNAs in the hippocampus and 2561 lncRNAs and 17,464 mRNAs expressed in the PFC. The lncRNAs identified correspond to ~14% of the transcriptome of the hippocampus and PFC and ~70% of the lncRNAs annotated in the mouse genome (NCBIM37) and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that a few of the tested lncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic lncRNA expression signatures. These results reveal an unexpected complexity of the lncRNA expression in the mouse brain.
尽管长非编码 RNA（lncRNA）在调节生物功能方面具有重要意义，但哺乳动物大脑亚区和神经元群体中 lncRNA 的表达谱在很大程度上仍未被描述。通过分析 RNA-seq 数据集，我们证明了 lncRNA 和 mRNA 在小鼠海马体和前额叶皮层（PFC）中的特定区域富集，这两个大脑区域主要参与记忆存储和神经精神疾病。我们在海马体中鉴定了 2759 个 lncRNA 和 17859 个 mRNA，在 PFC 中鉴定了 2561 个 lncRNA 和 17464 个 mRNA。鉴定的 lncRNA 对应于海马体和 PFC 转录组的约 14%，以及在小鼠基因组（NCBIM37）中注释的约 70%的 lncRNA，并沿着染色体作为不同数量的簇定位。重要的是，我们还发现一些共享基因组位置的测试 lncRNA-mRNA 对以特定的区域特异性方式显示特定的共表达。此外，我们发现大脑的亚区和特定的神经元群体具有特征性的 lncRNA 表达特征。这些结果揭示了小鼠大脑中 lncRNA 表达的出人意料的复杂性。
