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. Overall design: 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）在发育过程中随时间推移不断改变其分化潜能，依次产生不同的细胞类型。目前已发现诸多调控皮层发育的基因，但这些基因的时序表达调控机制仍不甚明晰。近年来研究证实，长链非编码RNA（long non-coding RNAs, lncRNAs）在诸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（strand-specific RNA sequencing）技术，揭示了大量长链非编码RNA在小鼠皮层发育过程中呈动态激活且差异表达的特征。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。值得注意的是，小鼠早期神经发生过程中皮层转录组发生了显著变化。皮层长链非编码RNA往往转录自与神经发育相关的蛋白编码基因邻近的基因组位点。最后，本研究发现大量预测的增强子区域能够转录产生RNA。本研究将有助于我们从分子层面更好地理解皮层神经前体细胞在发育过程中的命运决定机制，特别是长链非编码RNA在该过程中的作用。实验整体设计：采用Illumina HiSeq 2000测序平台，对胚胎发育第10.5天（E10.5）与第12.5天（E12.5）的小鼠胚胎背侧前脑（皮层）组织进行核糖体去除处理后构建RNA文库并获取转录组图谱，最终共获得4.1亿条双端测序读段。