Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary constraint, a hallmark of functionality. Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures. Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development. This led us to the hypothesis that spatiotemporal co-expression of ncRNAs and nearby protein-coding genes represents a general phenomenon, a prediction that was confirmed subsequently by in situ hybridisation in developing and adult mouse brain. We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

除编码蛋白质的信使RNA（messenger RNA, mRNA）外，真核转录组还包含大量转录自蛋白质编码基因座之外、功能未知的长非编码RNA（long non-protein-coding RNAs, ncRNAs）。本研究共鉴定出659个基因间区长非编码RNA，其基因组序列均呈现进化约束这一功能标志性特征。在该集合中，脑组织表达的长非编码RNA序列保守性更为显著，且显著富集预测的RNA二级结构。此外，脑组织表达的长非编码RNA优先定位于邻近的编码蛋白质基因旁，这类基因具备两项特征：其一，同样在脑组织中表达；其二，参与转录调控或神经系统发育过程。这一发现促使我们提出假说：长非编码RNA与邻近编码蛋白质基因的时空共表达是一种普遍现象，该假说随后通过发育中和成年小鼠脑组织的原位杂交实验得到了验证。我们将全部受进化约束的长非编码RNA集合作为重要的实验资源进行了共享，并首次提出了实质性且具有预测性的筛选标准，用于在研究长非编码RNA与mRNA转录本对的生物学功能及其对发育和疾病的贡献时开展优先排序工作。