Nuclear RNA in the nervous system

Background: Recent characterization of the transcriptional landscape of cell lines and whole tissues has suggested widespread transcription of the genome, including loci that produce regulatory non-coding RNAs that function within the nucleus. Methods: Here, we have defined the nuclear transcriptional landscape of the three major cellular divisions of the nervous system using flow sorting of genetically labeled nuclei from bacTRAP mouse lines followed by characterization the unique expression of coding, non-coding and intergenic RNAs in the mature mouse brain with RNAseq, and validation with independent methods. Results: Our findings reveal diverse expression across the cell-types of all classes of RNAs, including long non-coding RNAs - several of which were confirmed as highly enriched in the nuclei of specific cell-types using anatomical methods. Finally, we also discovered several examples of cell-type specific expression of tandem gene fusions, and report the first cell-type specific expression of circular RNAs, notably a neuron specific and nuclear enriched RNA arising from the gene Hnrnpu. Conclusion: These non-coding RNA expression data should provide an important context for studies evaluating the function of a variety of ncRNA in the nervous system. Overall design: Three to four independent replicate samples (each from one mouse) were collected for each of three sample types: Neuronal nuclear RNA, Astrocyte nuclear RNA, Oligodendrocyte nuclear RNA. Controls include low-coverage presorted nuclear RNA from each mouse.研究背景：近年来针对细胞系及完整组织转录组全景的表征研究表明，基因组存在广泛转录现象，其中包含在细胞核内发挥功能的调控性非编码RNA（non-coding RNA, ncRNA）编码基因座。研究方法：本研究通过对bacTRAP转基因小鼠品系的遗传标记细胞核进行流式分选，结合RNA测序（RNA-seq）对成熟小鼠脑内编码RNA、非编码RNA及基因间区RNA的特异性表达进行表征，并通过独立实验方法完成验证，从而明确了神经系统三大主要细胞类别的细胞核转录组全景。研究结果：本研究揭示了各类RNA在不同细胞类型中的多样化表达模式，其中长链非编码RNA（long non-coding RNA, lncRNA）有多个经解剖学方法验证，在特定细胞类型的细胞核中高度富集。此外，本研究还发现了若干串联基因融合的细胞类型特异性表达案例，并首次报道了环状RNA（circular RNA, circRNA）的细胞类型特异性表达现象，其中尤为值得关注的是由Hnrnpu基因编码的、神经元特异性且细胞核富集的RNA。研究结论：本研究产生的非编码RNA表达数据，可为后续探索各类非编码RNA在神经系统中的功能提供重要的研究背景。实验整体设计：针对三类样本类型——神经元细胞核RNA、星形胶质细胞核RNA、少突胶质细胞核RNA，各收集3至4份独立重复样本（每份样本均来自单只小鼠）。对照样本为每只小鼠预先分选的低覆盖度细胞核RNA。