Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data

Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.

长链非编码RNA（Long non-coding RNAs，lncRNAs）作为一类关键的非编码RNA家族，已受到广泛关注。尽管lncRNAs已在高等哺乳动物中完成功能注释与系统性研究，但目前得到系统鉴定与注释的lncRNAs仍寥寥无几。由于表达具有特异性，目前在胚胎脑组织中被鉴定的已知lncRNAs仍然十分有限。鉴于大量lncRNAs仅在脑组织中转录，因此针对发育中脑组织的lncRNAs研究具有特殊的研究价值。本研究通过定制化分析流程，整合公开可得的胚胎脑组织RNA测序（RNA-sequencing，RNA-seq）数据，鉴定出数千个胚胎脑组织lncRNAs。相当比例的新型转录本未被现有基因组资源所注释。相较于已知编码基因，推定的胚胎脑组织lncRNAs长度更短、剪接事件更少，且保守性更低。推定的lncRNAs的平均表达量仅为已知编码基因的十分之一，但与已知lncRNAs的表达水平相当。通过染色质数据分析发现，推定的胚胎脑组织lncRNAs与活性染色质标记相关，这一特征与已知lncRNAs一致。研究还表明，胚胎脑组织特异性表达的lncRNAs在成体脑组织中虽表达量较低，但仍存在表达。对推定的胚胎脑组织lncRNAs进行基因本体（Gene Ontology，GO）富集分析显示，其与脑发育过程密切相关。即便这些推定的lncRNAs本身被鉴定为印记lncRNAs，它们仍可能在基因组印记调控中发挥顺式调控作用。对一项基因敲低（knockdown）数据集的重新分析显示，有四种调控因子与lncRNAs存在关联。综上，对推定的lncRNAs进行鉴定与系统性分析，将为尚未被注释的小鼠非编码区域研究以及其与哺乳动物胚胎脑发育的关联提供全新的视角。