miRNA研究的计算机方法

MicroRNAs(miRNAs)是一类最新发现能够调控基因表达的非编码RNA,其内源长大约为21～23个核苷酸。miRNAs通过直接剪切靶基因mRNAs或者抑制翻译在后转录水平调控基因表达。一系列研究表明,他们在细胞分化、细胞生长、细胞迁移和细胞凋亡中发挥重要作用。由于miRNAs研究的实验方法耗时、耗材和效率低,所以计算机方法成为了miRNAs研究的替代方法。大部分与miRNA研究相关的计算机方法可以分为三类:miRNAs基因识别、miRNAs靶基因预测和miRNA-mRNA调控模块的预测。归纳miRNAs基因识别、miRNAs靶基因预测和miRNA-mRNA调控模块预测的原理,提供在这个领域已经提出来的特定计算机方法。     

Identification and Functional Analysis of MicroRNAs and Their Targets in Platanus acerifolia under Lead (Pb) Stress

MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in improving the urban ecological environment. MiRNAs that respond to abiotic stresses have been identified in plants; however, until now, the influence of Pb stress on P. acerifolia miRNAs has not been reported. To identify miRNAs and predict their target genes under Pb stress, two small RNA and two degradome libraries were constructed from Pb-treated and Pb-free leaves of P. acerifolia seedlings. After sequencing, 55 known miRNAs and 129 novel miRNAs were obtained, and 104 target genes for the miRNAs were identified by degradome sequencing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to predict the functions of the targets. The expressions of eight differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report about P. acerifolia miRNAs and their target genes under Pb stress. This study has provided data for further research into molecular mechanisms involved in resistance of P. acerifolia to Pb stress.     

花生miRNA与其靶基因的生物信息学预测

本研究利用生物信息学方法预测花生中的miRNA及其靶基因。将miRBase注册的已知植物miRNA与花生EST和GSS数据库进行比对搜索,筛选得到13条miRNA,进一步预测得到20个靶基因。分析结果显示大多数靶基因属于转录因子,调控植物的生长发育等多种生物过程。     

MicroRNA expression profile and lipid metabolism characteristics in liver of rat undergoing high-fat diet

This study aimed to investigate the microRNA expression profile and the characteristics of lipid metabolism in the livers of rats undergoing a high-fat diet. Fifty male Sprague-Dawley (SD) rats were divided into a standard chow group (C group, N = 10) and a high-fat diet group (H group, N = 40). After 12 weeks, the rat body weight, body length, fat mass, and serum lipid concentration were measured. The expression profile of microRNAs and the gene and protein expression levels involved in lipid metabolism in rat liver were detected. Body fat and serum lipid concentrations were all significantly higher in the H group than those in the C group (p < 0.05 or p < 0.01). The expression of 10 microRNAs showed significant differences in the liver (p < 0.05). In particular, the let-7 family expression levels significantly increased (p < 0.05) in the H group compared with those in the C group. Compared with the C group, the high-fat diet resulted in low FAS, CPT1A, and ApoAI mRNA expression levels (p < 0.05 or p < 0.01) and high PPARα and FAT/CD36 mRNA expression levels in the H group rat liver (p < 0.01). Meanwhile, the protein PPARα, FAS, CPT1A, FAT/CD36, and ApoAI expression levels were all significantly lower in the H group than those in the C group (p < 0.05 or p < 0.01). In conclusion, the high-fat diet increased the body fat and serum lipid levels and altered the 10 microRNA expression levels in the liver. The high-fat diet may affect hepatic carbohydrate metabolism and increase ectopic fat accumulation through let-7 family overexpression. The high-fat diet for 12 weeks decreased lipid metabolism level in the liver, thereby decreasing fatty acid synthesis, oxidation, and transport by down-regulating the PPARα, FAS, CPT1A, FAT/CD36, and ApoAI protein levels.     

Navigating the genomic instability mine field of osteosarcoma to better understand implications of non-coding RNAs

Osteosarcoma is one of the most genomically complex cancers and as result, it has been difficult to assign genomic aberrations that contribute to disease progression and patient outcome consistently across samples. One potential source for correlating osteosarcoma and genomic biomarkers is within the non-coding regions of RNA that are differentially expressed. However, it is unsurprising that a cancer classification that is fraught with genomic instability is likely to have numerous studies correlating non-coding RNA expression and function have been published on the subject. This review undertakes the formidable task of evaluating the published literature of non-coding RNAs in osteosarcoma. This is not the first review on this topic and will certainly not be the last. The review is organized with an introduction into osteosarcoma and the epigenetic control of gene expression before reviewing the molecular function and expression of long non-coding RNAs, circular RNAs, and short non-coding RNAs such as microRNAs, piwi RNAs, and short-interfering RNAs. The review concludes with a review of the literature and how the biology of non-coding RNAs can be used therapeutically to treat cancers, especially osteosarcoma. We conclude that non-coding RNA expression and function in osteosarcoma is equally complex to understanding the expression differences and function of coding RNA and proteins; however, with the added lens of both coding and non-coding genomic sequence, researchers can begin to identify the patterns that consistently associate with aggressive osteosarcoma.     

生物信息学中的MicroRNA预测研究

为microRNA预测的研究提供参考,讨论了生物信息学中有关MicroRNA预测研究的若干问题。根据最新的研究成果,由MicroRNA预测的特征信息和数据源,从结构序列分析方法、比较基因组方法和机器学习方法等方面对MicroRNA预测的生物信息学方法做了回顾和展望,指出了该领域研究的趋势。通过对3类方法的比较结果表明,采用机器学习方法的效果更优越,能较精确地预测出MicroRNA。     

基于电化学分析法定量检测MicroRNA的生物传感器

就miNA电化学法检测中探针材料选择、信号放大方式、电极传感界面调控以及电化学检测方法在研究辐射对miRNA表达的影响方面的潜在应用等方面进行综述。     

MicroRNA let-7表达调控机制研究进展

MicroRNA let-7调控干细胞分化、调节发育,抑制肿瘤发生发展,这些功能与let-7的表达水平密切相关。研究发现,Lin28、组蛋白去甲基化酶、miR-107和NF90-NF45复合物在转录和转录后水平调控let-7的表达;也存在一些Lin28依赖和Lin28非依赖的调控环路,调节let-7的表达。本文就let-7的调控机制研究进行综述。