Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles

Over the last years, the microRNA (miRNA) pathway has emerged as a key component of the regulatory network of pluripotency. Although clearly distinct states of pluripotency have been described in vivo and ex vivo, differences in miRNA expression profiles associated with the developmental modulation of pluripotency have not been extensively studied so far. Here, we performed deep sequencing to profile miRNA expression in naive (embryonic stem cell [ESC]) and primed (epiblast stem cell [EpiSC]) pluripotent stem cells derived from mouse embryos of identical genetic background. We developed a graphical representation method allowing the rapid identification of miRNAs with an atypical profile including mirtrons, a small nucleolar RNA (snoRNA)-derived miRNA, and miRNAs whose biogenesis may differ between ESC and EpiSC. Comparison of mature miRNA profiles revealed that ESCs and EpiSCs exhibit very different miRNA signatures with one third of miRNAs being differentially expressed between the two cell types. Notably, differential expression of several clusters, including miR290-295, miR17-92, miR302/367, and a large repetitive cluster on chromosome 2, was observed. Our analysis also showed that differentiation priming of EpiSC compared to ESC is evidenced by changes in miRNA expression. These dynamic changes in miRNAs signature are likely to reflect both redundant and specific roles of miRNAs in the fine-tuning of pluripotency during development.     

miR-290家簇在小鼠胚胎干细胞中的表达与调控功能

微RNA（microRNA,miRNA）是一类约22nt的非编码小分子RNA,主要在转录后水平负调控基因表达,其在生物发商、疾病、肿瘤中行使着重要调控作用。胚胎干细胞（embryonic stem cell,ESC）具有发育的全能性,能分化出成体动物的所有组织和器官。研究和利用ESC是当前生物工程领域的热点之一。近年来,越来越多的研究表明,miRNA在ESC的自我更新、分化、命运决定等方面行使着重要的调控作用。其中,miR-290家簇是在鼠科动物ESC中特异且高表达的miRNA。本文综述了miR-290家簇在ESC中的表达、功能及其分子调控网络方面的研究进展。     

Suppression of epithelial–mesenchymal transition and apoptotic pathways by miR-294/302 family synergistically blocks let-7-induced silencing of self-renewal in embryonic stem cells

The embryonic stem cell (ESC)-enriched miR-294/302 family and the somatic cell-enriched let-7 family stabilizes the self-renewing and differentiated cell fates, respectively. The mechanisms underlying these processes remain unknown. Here we show that among many pathways regulated by miR-294/302, the combinatorial suppression of epithelial–mesenchymal transition (EMT) and apoptotic pathways is sufficient in maintaining the self-renewal of ESCs. The silencing of ESC self-renewal by let-7 was accompanied by the upregulation of several EMT regulators and the induction of apoptosis. The ectopic activation of either EMT or apoptotic program is sufficient in silencing ESC self-renewal. However, only combined but not separate suppression of the two programs inhibited the silencing of ESC self-renewal by let-7 and several other differentiation-inducing miRNAs. These findings demonstrate that combined repression of the EMT and apoptotic pathways by miR-294/302 imposes a synergistic barrier to the silencing of ESC self-renewal, supporting a model whereby miRNAs regulate complicated cellular processes through synergistic repression of multiple targets or pathways.Embryonic stem cells (ESCs) can self-renew indefinitely and differentiate into any cell type.¹ Therefore, they hold great potential for clinical applications in regenerative medicine. However, the molecular mechanisms regulating the self-renewal and differentiation of ESCs are still not fully understood. miRNAs are an important class of short non-coding RNAs that regulate ESC self-renewal and differentiation.² miRNA-deficient ESCs proliferate at a slower rate with a slight accumulation of cells in the G1 phase, and they cannot silence the self-renewal program when induced to differentiate.^{3, 4, 5} Introducing individual members from an miRNA family highly expressed in ESCs partially rescues the proliferation defect and reverses the G1 accumulation.⁶ The family shares a seed sequence (5′-AAGUGCU-3′) and has eight members, including miR-294 and miR-302a-d. Because of their role in influencing the ESC Cell Cycle, they have been called the ESCC family of miRNAs. In addition, ESC cell cycle regulating miRNAs (ESCC miRNAs) suppress the G1 restriction point by inhibiting retinoblastoma (Rb) family proteins, preventing ESCs from exiting the cell cycle during serum starvation or contact inhibition.⁷ In contrast to ESCC miRNAs, the introduction of let-7 family miRNAs that are enriched in somatic cells as well as several other lineage-specific miRNAs such as miR-26a, miR-99b, miR-193, miR-199a-5p, and miR-218 silences self-renewal in Dgcr8−/− (DiGeorge syndrome critical region gene 8−/−) ESCs but not wild-type ESCs.^{7, 8} Interestingly, the ESCC miRNAs prevent these miRNAs from silencing ESC self-renewal. Consistent with their roles in promoting self-renewal, ESCC miRNAs dramatically enhance the de-differentiation of human and mouse fibroblasts to induced pluripotent stem cells (iPSCs).^{9, 10, 11, 12, 13}How ESCC miRNAs maintain self-renewal in the presence of differentiation-inducing miRNAs is not clearly understood. Genomic studies have shown that these miRNAs target hundreds of mRNAs enriched in many biological processes.^{8, 14, 15, 16} Functional analysis of a small number of targets chosen based on their known roles has begun to give some insights into their functions in reprogramming somatic cells to iPSCs.^{10, 11, 17} However, due to the inherent differences between the maintenance and establishment of pluripotency,¹⁸ what targets or pathways underlie the antagonism between the two opposing families of miRNAs in regulating ESC self-renewal remains unknown. Recent work showed that while the miR-294/302 family suppresses and let-7 induces the G1/S restriction point, this cell cycle function cannot explain their antagonistic roles in maintaining pluripotency.⁷ Therefore, we set out to search for additional functions of the two miRNA families that directly underlie their opposing roles in regulating pluripotency. In this study, we found that combined repression of epithelial–mesenchymal transition (EMT) and apoptotic pathways by miR-294/302 forms a synergistic barrier to block the silencing of ESC self-renewal by let-7 and other differentiation-inducing miRNAs.     

MicroRNA signatures of iPSCs and endoderm-derived tissues

MicroRNAs (miRNAs), small non-coding RNAs that fine-tune gene expression, play multiple roles in the cell, including cell fate specification. We have analyzed the differential expression of miRNAs during fibroblast reprogramming into induced pluripotent stem cells (iPSCs) and endoderm induction from iPSCs upon treatment with high concentrations of Activin-A. The reprogrammed iPSCs assumed an embryonic stem cell (ESC)-like miRNA signature, marked by the induction of pluripotency clusters miR-290–295 and miR-302/367 and conversely the downregulation of the let-7 family. On the other hand, endoderm induction in iPSCs resulted in the upregulation of 13 miRNAs. Given that the liver and the pancreas are common derivatives of the endoderm, analysis of the expression of these 13 upregulated miRNAs in hepatocytes and pancreatic islets revealed a tendency for these miRNAs to be expressed more in pancreatic islets than in hepatocytes. These observations provide insights into how differentiation may be guided more efficiently towards the endoderm and further into the liver or pancreas. Moreover, we also report novel miRNAs enriched for each of the cell types analyzed.     

MicroRNA-302/367 cluster功能的研究进展

MircroRNA (miRNA)是一段长度约为22个nt的小型非编码RNA,广泛存在于真核生物中,具有调节基因表达的作用。对miRNA的鉴定、功能分析和调控机理研究已成为当今生物领域的热点。miR-302/367cluster属于胚胎干细胞特异性细胞周期调控miRNAs家族成员(embryonic stem cell-specific cell cycle-regulating family of microRNAs,ESCC miRNAs),通常由5个成员miR-302a、miR-302b、miR-302c、miR-302d及miR-367组成,大多分布在脊椎动物中。研究表明,该miRNAs簇对细胞多种生理过程起重要调控作用,如人胚胎干细胞(hESCs)多能性的维持、自我更新等。本研究概述了miRNA的合成及作用机理,ESCC miRNAs促进体细胞再程序化,并总结了miR-302/367 cluster在细胞周期调控、表观遗传修饰及一些细胞信号转导途径中的作用,为采用该类miRNAs诱导体细胞再程序化为iPS细胞(Induced pluripotent stem cells)提供一定的理论基础。     

The role of miRNAs and endogenous siRNAs in maternal‐to‐zygotic reprogramming and the establishment of pluripotency

RNA silencing is a complex of mechanisms that regulate gene expression through small RNA molecules. The microRNA (miRNA) pathway is the most common of these in mammals. Genome‐encoded miRNAs suppress translation in a sequence‐specific manner and facilitate shifts in gene expression during developmental transitions. Here, we discuss the role of miRNAs in oocyte‐to‐zygote transition and in the control of pluripotency. Existing data suggest a common principle involving miRNAs in defining pluripotent and differentiated cells. RNA silencing pathways also rapidly evolve, resulting in many unique features of RNA silencing in different taxonomic groups. This is exemplified in the mouse model of oocyte‐to‐zygote transition, in which the endogenous RNA interference pathway has acquired a novel role in regulating protein‐coding genes, while the miRNA pathway has become transiently suppressed.     

Live isolation of naïve ESCs via distinct glucose metabolism and stored glycogen

Naïve and primed pluripotent stem cells recapitulate the peri- and post-implantation development, respectively. Thus, investigation of distinct traits between each pluripotent stem cell type would shed light on early embryonic processes. Herein, by screening a fluorescent probe library, we found that intracellular glycogen led to specific reactivity to CDg4, a glycogen fluorescence sensor, in both human and mouse naïve embryonic stem cells (ESCs). The requirement of constant inhibition of Gsk3β as well as high oxidative phosphorylation (OxPHOS) in naïve compared to primed ESCs was closely associated to high level of intracellular glycogen in naïve ESCs. Both capacity of OxPHOS and stored glycogen, rescued naïve ESCs by transient inhibition of glycolysis, which selectively eliminated primed ESCs. Additionally, naïve ESCs with active OxPHOS were enriched from a mixture with primed ESCs by high reactivity to ATP-Red1, a mitochondrial ATP fluorescence probe. These results indicate the active OxPHOS and high intracellular glycogen as a novel “biomarker” delineating metabolic remodeling during the transition of naïve pluripotency.     

The expanding role of miR-302–367 in pluripotency and reprogramming

MicroRNA (miRNA) has been shown to be essential for regulating cell fate and pluripotency; however, our knowledge of miRNA function in stem cells is incomplete due to experimental limitations and difficulties in identifying their physiological targets. Recent studies implicated hESC-expressed miRNAs (miR?302–367 and miR?371–373 clusters) in regulating BMP signaling and promoting pluripotency, suggesting that low levels of BMP signaling may promote pluripotency by preventing neural induction. A comprehensive list of miR?302–367 targets recently identified by genome-wide approaches suggests a number of additional cellular processes and signaling pathways whose regulation by miR?302–367 may promote pluripotency and reprogramming, such as cell cycle, epigenetic changes, metabolism and vesicular transfer.     

MicroRNA对胚胎干细胞的多能性网络调控

胚胎干细胞(Embryonic stem cells, ESCs)是一类能够无限增殖和诱导分化为多种类型细胞的干细胞。MicroRNA(miRNA)是一类内源性具有调控基因表达功能的非编码RNA, 在ESCs增殖和分化过程中起重要作用。MiRNA可以通过对ESCs多能性网络中的转录因子、细胞周期、表观遗传学、信号转导等方面调控, 促使ESCs维持多能性状态。文章重点综述了miRNA的生成过程、调控ESCs多能性的主要miRNA家族以及miRNA对ESCs多能性网络调控作用等内容。