Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells

BackgroundMicroRNAs (miRNAs: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence).Methodology/Principal FindingsIn order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer?/?) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF?/?) cells, which display loss of repression of pluripotence genes upon differentiation.Conclusion/SignificanceCombining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF?/?) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.

背景 微小RNA（MicroRNAs, miRNAs）是一类短链非编码RNA，现已成为转录后基因调控的关键因子以及基因网络的核心组成部分。miRNAs与干细胞密切相关，而干细胞在发育过程中具备显著的双重功能：既可通过自我更新（self-renewal）实现持续自我增殖，也可分化为仅能执行特定有限功能的细胞（多能性，pluripotence）。
方法与主要发现 为从发育的窄窗口期内鉴定新型miRNAs，我们针对成人组织祖细胞的转录本序列开展了硅基（in silico）微保守元件（micro-conserved elements, MCE）搜索。本次分析揭示了大量此前未被报道的miRNA候选序列，其中包含545种相较于成体细胞，在胚胎干细胞（embryonic stem cells, ES cells）中富集的小RNA。约20%的这类新型候选序列在miRNA成熟功能缺陷的ES（Dicer⁻/⁻）细胞中表达下调。在视黄酸（retinoic acid, RA）诱导的ES细胞分化过程中，富集于ES细胞的miRNA候选序列的表达趋势，与成年组织中丰度较高的mmu-mirs类RNA呈现出显著且相反的变化模式。在ES（GCNF⁻/⁻）细胞中，miRNA及新型候选序列的表达趋势均发生显著扰动，这类细胞在分化过程中会丧失对多能性基因的抑制作用。
结论与意义 结合表达谱信息与miRNA靶标预测结果，我们鉴定出了与ES细胞多能性及分化相关的miRNA-mRNA调控对。这些调控对在ES（GCNF⁻/⁻）突变体中的表达扰动，提示miRNA在调控ES细胞自我更新、多能性与分化的核心基因网络中发挥重要作用。