Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex

Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.长链非编码RNA（long non-coding RNA，lncRNA）在诸多生物学过程中发挥关键调控作用。阐明lncRNA在器官发育阶段的细胞类型特化功能，需获取其在单个祖细胞群而非整体组织中的表达数据。为在大脑皮层发育过程中达成这一研究目标，我们采用双报告基因小鼠品系，分离得到共存的增殖性神经干细胞、正在分化的神经源性祖细胞与新生神经元，并通过双端高通量测序技术分析lncRNA的表达水平。本研究共鉴定出379个编码新型lncRNA的基因组位点，并对迄今已报道的全部已注释及新型lncRNA的细胞特异性表达模式开展了全面评估。本研究为探究干细胞定向分化及神经发生过程中的这类难以研究的转录本提供了极具价值的全新资源。本数据集涵盖胚胎发育第14.5天小鼠胚胎外侧皮层的三类细胞——增殖性祖细胞、分化中的祖细胞及神经元的mRNA表达谱，每类细胞均设置3次生物学重复。