Transcriptome analysis of mouse cortical development and characterization of long non-coding RNAs

Cortical neural progenitor cells (NPCs) change their competency over time during development, giving rise to distinct cell types sequentially. Many genes that govern cortical development are now known, but it remains elusive how their temporal expression is controlled. Recently, long non-coding RNAs are found to be essential for cell-fate specification and precise gene regulation in many developmental events. In this study, strand-specific RNA sequencing studies unveil large amount of long non-coding RNAs are actively and differentially expressed across mouse cortical development. Integration of RNA sequencing data from key stages of developing mouse cortex enables us to cluster coding and non-coding transcripts into co-expression "modules" to infer functional relationships. Intriguingly, the cortical transcriptome undergoes significant changes in early mouse neurogenesis. Cortical long non-coding RNAs tends to be transcribed from genomic loci adjacent to protein-coding genes related to neural development. Finally, we found large amount of predicted enhancer regions are able to transcribe RNAs. This study will help us better understand molecularly how cortical NPCs specify their fates during development, especially roles of lncRNAs in this process. Ribosomal-depletion RNA profiles of dorsal forebrain (cortex) tissues from E10.5 and E12.5 mouse embryos were generated using Illumina HiSeq 2000 and totally 410 million paired-end reads were generated.皮层神经前体细胞（cortical neural progenitor cells, NPCs）在发育进程中随时间推移动态改变其功能潜能，依次产生多种不同的细胞类型。目前已鉴定出诸多调控皮层发育的基因，但其时序表达的调控机制仍未明确。近年来研究表明，长链非编码RNA（long non-coding RNAs, lncRNAs）在众多发育事件中对细胞命运决定与精准基因调控发挥关键作用。本研究通过链特异性RNA测序技术，发现大量长链非编码RNA在小鼠皮层发育过程中呈活跃且差异的表达特征。整合小鼠皮层发育关键阶段的RNA测序数据，我们可将编码与非编码转录本聚类为共表达模块，进而推断其功能关联。值得关注的是，小鼠早期神经发生阶段的皮层转录组发生了显著变化。皮层长链非编码RNA通常转录自与神经发育相关蛋白编码基因相邻的基因组区域。最后，本研究证实大量预测得到的增强子区域能够转录生成RNA。本研究有助于从分子层面阐明皮层神经前体细胞在发育过程中的命运决定机制，尤其揭示长链非编码RNA在该过程中的功能。本研究采用Illumina HiSeq 2000测序平台，对E10.5与E12.5小鼠胚胎的背侧前脑（皮层）组织开展核糖体RNA去除处理的RNA谱分析，共获得4.1亿条双端测序读段。