共查询到20条相似文献,搜索用时 31 毫秒
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Jinpo Sui Qingkuan Liu Hongyan Zhang Ying Kong 《Journal of cellular biochemistry》2019,120(6):9631-9638
Chondrosarcoma (CHS) is a common malignant bone sarcoma and its occurrence increases with age. microRNAs (miRNAs) are a class of noncoding RNAs that participate in various biological processes and disease pathogenesis by targeting functional messenger RNA (mRNA). However, the modulation of miRNAs in CHS remains largely unknown. In this study, we performed integrative analysis to explore the expression profiles of miRNAs and mRNAs, together with their interaction networks in human CHS tissues and cell lines by RNA-seq (miRNA and mRNA). A total of 133 and 796 differentially expressed miRNAs and mRNAs were identified (|Fold change| ≥ 2 and P-value ≤ 0.5). miRNA-mRNA regulatory interactions between 55 miRNAs and 242 mRNAs were screened by the Pearson correlation analysis and target prediction. mRNAs in the network were enriched to 145 Gene Ontology terms and 35 Kyoto Encyclopedia of Genes and Genomes pathways. Specifically, some key regulators (hub-miRNAs) in the network (miR-622, miR-4539, miR-145, miR-25, and miR-96) were suggested to play important regulatory roles in the pathogenesis of CHS. In addition, functional experiments validated that miR-622 regulated CHS cell proliferation by targeting bone morphogenetic protein 1 (BMP1). 相似文献
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微RNA(microRNA,miRNA)是一类在分子进化中十分保守的非编码RNA,长度约22个核苷酸,一般情况下它在转录后水平抑制基因表达。miRNA在细胞增殖、分化、凋亡等诸多生理过程中发挥着重要作用。有些miRNA具有组织特异性表达,其中miR-206是目前发现的唯一在骨骼肌中特异表达的miRNA,它在调节骨骼肌发生过程中扮演重要角色。miR-206表达异常与一些肌肉相关疾病如肌肉营养不良、肌萎缩性侧索硬化症等有关。此外,在Texel羊中,myostatin基因的一个点突变就产生了一个miR-206和miR-1的靶点,抑制了myostain基因的表达,从而产生了双肌表型。因此,miR-206有可能成为治疗肌肉相关疾病和畜禽改良育种的重要候选分子。 相似文献
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Peng Zhou Weiyi Xu Xueling Peng Zhenhua Luo Qinghe Xing Xulin Chen Chengqian Hou Weihong Liang Jianwen Zhou Xiaoyan Wu Zhou Songyang Songshan Jiang 《PloS one》2013,8(7)
Animal microRNA (miRNA) target prediction is still a challenge, although many prediction programs have been exploited. MiRNAs exert their function through partially binding the messenger RNAs (mRNAs; likely at 3′ untranslated regions [3′UTRs]), which makes it possible to detect the miRNA-mRNA interactions in vitro by co-transfection of miRNA and a luciferase reporter gene containing the target mRNA fragment into mammalian cells under a dual-luciferase assay system. Here, we constructed a human miRNA expression library and used a dual-luciferase assay system to perform large-scale screens of interactions between miRNAs and the 3′UTRs of seven genes, which included more than 3,000 interactions with triplicate experiments for each interaction. The screening results showed that the 3′UTR of one gene can be targeted by multiple miRNAs. Among the prediction algorithms, a Bayesian phylogenetic miRNA target identification algorithm and a support vector machine (SVM) presented a relatively better performance (27% for EIMMo and 24.7% for miRDB) against the average precision (17.3%) of the nine prediction programs used here. Additionally, we noticed that a relatively high conservation level was shown at the miRNA 3′ end targeted regions, as well as the 5′ end (seed region) binding sites. 相似文献
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Background
MicroRNAs (miRNAs) are a class of endogenous small regulatory RNAs. Identifications of the dys-regulated or perturbed miRNAs and their key target genes are important for understanding the regulatory networks associated with the studied cellular processes. Several computational methods have been developed to infer the perturbed miRNA regulatory networks by integrating genome-wide gene expression data and sequence-based miRNA-target predictions. However, most of them only use the expression information of the miRNA direct targets, rarely considering the secondary effects of miRNA perturbation on the global gene regulatory networks.Results
We proposed a network propagation based method to infer the perturbed miRNAs and their key target genes by integrating gene expressions and global gene regulatory network information. The method used random walk with restart in gene regulatory networks to model the network effects of the miRNA perturbation. Then, it evaluated the significance of the correlation between the network effects of the miRNA perturbation and the gene differential expression levels with a forward searching strategy. Results show that our method outperformed several compared methods in rediscovering the experimentally perturbed miRNAs in cancer cell lines. Then, we applied it on a gene expression dataset of colorectal cancer clinical patient samples and inferred the perturbed miRNA regulatory networks of colorectal cancer, including several known oncogenic or tumor-suppressive miRNAs, such as miR-17, miR-26 and miR-145.Conclusions
Our network propagation based method takes advantage of the network effect of the miRNA perturbation on its target genes. It is a useful approach to infer the perturbed miRNAs and their key target genes associated with the studied biological processes using gene expression data.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-255) contains supplementary material, which is available to authorized users. 相似文献11.
MicroRNAs (miRNAs) have been implicated as regulators of central nervous system (CNS) development and function. miR-124 is an evolutionarily ancient, CNS-specific miRNA. On the basis of the evolutionary conservation of its expression in the CNS, miR-124 is expected to have an ancient conserved function. Intriguingly, investigation of miR-124 function using antisense-mediated miRNA depletion has produced divergent and in some cases contradictory findings in a variety of model systems. Here we investigated miR-124 function using a targeted knockout mutant and present evidence for a role during central brain neurogenesis in Drosophila melanogaster. miR-124 activity in the larval neuroblast lineage is required to support normal levels of neuronal progenitor proliferation. We identify anachronism (ana), which encodes a secreted inhibitor of neuroblast proliferation, as a functionally important target of miR-124 acting in the neuroblast lineage. ana has previously been thought to be glial specific in its expression and to act from the cortex glia to control the exit of neuroblasts from quiescence into the proliferative phase that generates the neurons of the adult CNS during larval development. We provide evidence that ana is expressed in miR-124-expressing neuroblast lineages and that ana activity must be limited by the action of miR-124 during neuronal progenitor proliferation. We discuss the possibility that the apparent divergence of function of miR-124 in different model systems might reflect functional divergence through target site evolution. 相似文献
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Xiangling Yang William W. Du Haoran Li Fengqiong Liu Anna Khorshidi Zina Jeyapalan Rutnam Burton B. Yang 《Nucleic acids research》2013,41(21):9688-9704
MicroRNAs (miRNA) precursor (pre-miRNA) molecules can be processed to release a miRNA/miRNA* duplex. In the canonical model of miRNA biogenesis, one strand of the duplex is thought to be the biologically active miRNA, whereas the other strand is thought to be inactive and degraded as a carrier or passenger strand called miRNA* (miRNA star). However, recent studies have revealed that miRNA* strands frequently play roles in the regulatory networks of miRNA target molecules. Our recent study indicated that miR-17 transgenic mice could abundantly express both the mature miR-17-5p and the passenger strand miR-17-3p. Here, we showed that miR-17 enhanced prostate tumor growth and invasion by increasing tumor cell proliferation, colony formation, cell survival and invasion. miRNA target analysis showed that both miR-17-5p and miR-17-3p repressed TIMP metallopeptidase inhibitor 3 (TIMP3) expression. Silencing with small interfering RNA against TIMP3 promoted cell survival and invasion. Ectopic expression of TIMP3 decreased cell invasion and cell survival. Our results demonstrated that mature miRNA can function coordinately with its passenger strand, enhancing the repressive ability of a miRNA by binding the same target. Within an intricate regulatory network, this may be among the mechanisms by which miRNA can augment their regulatory capacity. 相似文献
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