Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.
Nucleic Acids Res. 2012 Jul;40(13):6001-15. doi: 10.1093/nar/gks311. Epub 2012 Apr 6.
Protein-coding genes, guiding differentiation of ES cells into neural cells, have extensively been studied in the past. However, for the class of ncRNAs only the involvement of some specific microRNAs (miRNAs) has been described. Thus, to characterize the entire small non-coding RNA (ncRNA) transcriptome, involved in the differentiation of mouse ES cells into neural cells, we have generated three specialized ribonucleo-protein particle (RNP)-derived cDNA libraries, i.e. from pluripotent ES cells, neural progenitors and differentiated neural cells, respectively. By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs. In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation. About half of ncRNA sequences from the three cDNA libraries mapped to intergenic or intragenic regions, designated as interRNAs and intraRNAs, respectively. Thereby, novel ncRNA candidates exhibited a predominant size of 18-30 nt, thus resembling miRNA species, but, with few exceptions, lacking canonical miRNA features. Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.
过去，人们广泛研究了指导胚胎干细胞（ES 细胞）分化为神经细胞的蛋白编码基因。然而，对于 ncRNA 这一类，仅描述了一些特定的 microRNAs（miRNAs）的参与。因此，为了描绘在小鼠 ES 细胞分化为神经细胞过程中涉及的整个小非编码 RNA（ncRNA）转录组，我们分别从多能性 ES 细胞、神经祖细胞和分化的神经细胞中生成了三个专门的核糖核蛋白颗粒（RNP）衍生 cDNA 文库。通过高通量测序和转录谱分析，我们鉴定出了一些新的 miRNA 参与 ES 细胞分化，以及七个小核仁 RNA。此外，在 ES 细胞分化过程中，7SL、7SK 和 vault-2 RNA 的表达显著上调。来自这三个 cDNA 文库的约一半 ncRNA 序列映射到基因间或基因内区域，分别被指定为 interRNAs 和 intraRNAs。因此，新的 ncRNA 候选物表现出 18-30nt 的主要大小，因此类似于 miRNA 种类，但除了少数例外，缺乏典型的 miRNA 特征。此外，这些新的 intraRNAs 和 interRNAs 不仅在干细胞衍生物中表现出差异表达，而且在海马神经元和星形胶质细胞的原代培养物中也表现出差异表达，这增强了它们在神经 ES 细胞分化中的潜在功能。
