人类管家基因和非管家基因microRNA绑定密度的比较及与3′UTR进化保守性关系的分析

目的：该研究从整体水平比较microRNA（miRNA）对管家基因和非管家基因的调控差异并研究3′UTR的进化保守性与miRNA对两类基因调控差异之间的相关性。方法通过对3个基于序列的miRNA靶基因预测软件整合分析,并结合基于miRNA-靶基因的表达谱数据相关性分析,以获得miRNA对两类基因的调控情况,同时利用phastCons保守性分值对两类基因的3′UTR区域进行多物种进化分析。结果研究发现miRNA在管家基因的3′UTR上有显著地高密度绑定,管家基因的3′UTR区域具有相对较高的序列保守性。结论该研究结果突出了miRNA对管家基因表达调控的重要作用,对于重新理解miRNA对真核生物基因表达调控作用具有一定的参考价值。     

miRNA功能研究进展

miRNA是一类长度为20~25nt的小分子非编码RNA。在线虫、小鼠、人、植物等多种生物中已发现了数百种miRNA。无论在低等的线虫还是在高等的哺乳动物中，miRNA都起着调控基因表达的重要作用。生物信息学分析表明人类全部基因的三分之一都受到miRNA的调控。这表明，miRNA分子实际上是基因调控网络中的核心成分。近来研究发现miRNA与人类的某些疾病密切相关。本文对miRNA分子功能及其研究方法的进展做一概述。     

模拟失重下小鼠成骨细胞功能相关miRNA生物信息学预测

目的 应用生物信息学方法预测模拟失重环境下与小鼠成骨细胞功能变化相关的miRNAs.方法 收集并整理已报道的针对模拟失重环境下小鼠成骨细胞内mRNAs表达变化的基因芯片检测数据,分析差异表达显著的mRNAs,搜集其基因组定位信息;在miRBase数据库中查找处于这些基因组位置上的内含子miRNAs,并应用靶基因预测、GO富集分析和KEGG pathway富集分析进行后续miRNA功能预测.结果 鉴定出5种与宿主mRNA共处同一转录单元的潜在内含子miRNAs.结论 预测出的5种内含子miRNAs在模拟失重环境所致成骨细胞功能变化中具有潜在调控作用,为进一步实验研究提供数据支持和理论指导.     

宿主microRNA靶向介导的减毒活疫苗研究进展

疫苗是预防病毒性传染病的最有效手段,包括减毒活疫苗、灭活疫苗、核酸疫苗和基因工程疫苗等。减毒活疫苗模拟了病毒的感染过程,能有效诱导机体产生体液和细胞免疫应答,在临床上得到广泛应用。传统的减毒活疫苗一般通过连续传代获得,研发成本高。微小RNA（ microRNA,miRNA）靶向调节是新近发现的宿主调控基因表达的重要手段,具有明确的组织特异性和种属特异性。通过反向遗传学技术能够将特异的宿主miRNA靶向序列有效整合入病毒基因组,从而实现对病毒生物学特征的有效调节,在减毒活疫苗设计与研发领域有着良好的应用前景。该文综述了miRNA靶向介导的减毒策略及其在疫苗设计中的研究进展。     

电离辐射与microRNA

MicroRNA(miRNA)是一类18～24 nt的非编码RNA分子.miRNA普遍存在于生物界,具有高度的保守性,广泛参与细胞分化与发育、细胞凋亡、肿瘤发生等多方面的基因表达调控.Lee等~([1])首先发现Lin-4作为一种调控线虫发育的miRNA之后,科学家对miRNAs调控的基因表达进行了广泛深入的研究,到日前为止,成熟miRNAs的总数已达10 581种,其中,在人类基因组中已发现721种(miRBase 14.0:http://microrna.sanger.ac.uk/)~([2]).据推测,人类miRNA的     

动物胚胎发育中的MicroRNAs研究进展

MicroRNA（miRNA）是一类广泛存在于真核生物中的非编码RNA,具有调控功能,长度约有20～25个核苷酸,它通过与靶基因特异性的碱基配对引起靶基因的降解或者抑制其翻译,从而实现对靶基因的转录后表达的调控。文章综述了miRNA的发现、体内生成机制、作用机制及不同动物种类胚胎发育过程中miRNA的鉴定和研究．并并阐述了miRNA研究中的问题及应用前景。     

微小RNA在基因表达调控中的作用研究进展

微小RNA是近年来在多种真核生物及病毒中发现的一类长度为19-26nt(或bp)、具有基因表达调控作用的单链或双链RNA分子。目前已发现的微小RNA分子包括siRNA、miRNA以及新近发现的调节性小RNA(small modulatory RNA，smRNA)。它们具有基因表达调控等重要作用，因而受到了较为广泛的关注。本文对3种微小RNA在基因表达调控方面的作用作一综述。     

miRNA介导的病毒-人相互作用研究进展

微小RNA（microRNA,miRNA）是一类内源性,长度约为22核苷酸的单链RNA分子,可通过5′端的种子区与靶标转录本mRNA的3′UTR配对,导致靶mRNA的降解或翻译抑制。越来越多的研究发现,miRNA在介导病毒-人相互作用过程中发挥着重要的作用,作用模式包括病毒miRNA靶向人及自身的转录本、人miRNA靶向病毒及自身的转录本、病毒的miRNA介导人miRNA调控的网络、RNA干扰（RNAi）相关和干扰素相关的宿主对病毒的抑制及反抑制。miRNA介导的病毒-人相互作用的研究对于全面理解病毒-宿主相互作用的机制、开发抗病毒的药物具有重要意义。     

新生小鼠与成年小鼠心肌环状RNA差异表达分析

目的 探讨新生小鼠（乳鼠）与成年小鼠（成鼠）心肌环状RNA(circRNA)的差异表达情况并阐明其可能的调控机制。方法 选取新生24 h内的雄性C57BL/6J乳鼠和8周龄C57BL/6J雄性成鼠各3只为研究对象。应用RNA提取和转录组芯片杂交的方法检测小鼠左心室组织circRNA的差异表达情况。应用GO和KEGG富集分析获得差异circRNA宿主基因的相关调控网络。分析差异表达circRNA的宿主基因和相互作用的miRNA调控分子。结果 芯片检测获得39个差异表达的circRNA,其中在乳鼠心脏组织中上调表达38个,下调表达1个。GO富集分析显示,上调表达的circRNA主要与蛋白激酶和RNA相关蛋白的反向激活调控有关,而这些宿主基因最主要的信号转导调控通路与有丝分裂调控、流体力学调控和硫基代谢调控有关（P均<0.001）。根据芯片分析结果,获取差异表达倍数>5的circRNA共有5个,分别是上调表达的mmu-circRNA-0001016、mmu-circRNA-0000126、mmu-circRNA-0000663、mmu-circRNA-0000914和下调表达的m...     

miRNA参与p53基因调控网络研究进展

在细胞增殖和细胞死亡等过程中均发现一些miRNA可以作为肿瘤抑制基因或癌基因参与调节。研究发现miR-34作为p53转录激活的靶分子,参与了包括细胞周期阻滞和细胞凋亡等过程的调节,miR-34的缺失可使p53介导的细胞效应受阻。miR-29可激活p53的表达并诱导p53介导的细胞凋亡。此外,还有许多miRNA分子受到p53的转录抑制。一种miRNA可调节多种不同的靶蛋白分子,因此大大拓展了p53调控网络的层面。越来越多的证据表明miRNA参与了癌基因和抑癌基因网络的调控,同时为肿瘤治疗提供了新的治疗策略。     

miRNA参与的动物发育调控研究进展

动物的发育是一个严格受控的复杂过程,需要在时空上精确控制相关基因的表达.miRNA通过抑制靶mRNA翻译或使之降解失稳从而在转录后降低基因的活性.近期的实验研究表明,miRNA在动物发育的诸多方面发挥着重要调控功能,并表现出特有的调控模式.本文对miRNA参与动物发育过程的调控研究进行了综述.     

60Co γ射线照射致小鼠肝脏的miRNAs表达改变

目的 应用miRNA芯片筛选4 Gy60Co γ射线照射后小鼠肝脏中差异表达的miRNAs,生物信息学方法探索差异表达miRNAs调控的主要功能.方法 SPF级C57BL/6J小鼠接受4 Gy60Co γ射线单次全身照射后,进行外周血白细胞计数和骨髓嗜多染红细胞微核计数.应用miRNA芯片筛选照射后小鼠肝脏中差异表达的miRNAs,用miRNA特异引物对部分差异表达miRNA进行实时定量PCR(real time PCR)验证.运用生物信息学方法,对差异miRNAs靶基因及调控功能进行预测.结果 4 Gyγ射线照射后,外周血白细胞总数与对照组相比显著减少(t=2.87,P＜0.05),而骨髓嗜多染红细胞微核率与对照组相比显著增加(t=-2.91,P＜0.05).miRNA芯片结果显示,照射组与对照组差异表达的miRNAs共17个,其中9个表达上调,8个表达下调.miR-124和miR-34a的实时荧光定量RT-PCR验证结果与芯片结果一致.GO分析发现,与黏附、细胞周期相关的通路被抑制,一些免疫相关通路被激活.结论 miR-34a和miR-194参与了急性辐射损伤的调控,起主要调控作用的miRNAs还有miR-124、miR-382和miR-92a*.

Abstract：

Objective To investigate the differential expression profiles of microRNAs in the liver of 60Co γ-ray irradiated mice using microRNA microarray and to explore their main functions by bioinformatic analysis.Methods After SPF C57BL/6J mice expose to 4 Gy-single whole body radiation,total number of peripheral WBC and the fMNPCE were measured at 3 d.The differentially expressed miRNAs in mouse liver were detected with miRNA microarray,miRNA-124 and miR-34a were confirmed by real time RT-PCR assay.Bioinformatic analysis was applied to explore target genes and the main functions of the differential expressed miRNAs.Results Compared with control group,the total number of peripheral WBC decreased( t = 2.87,P ＜ 0.05 ) ,while the fMNPCE in bone marrow increased ( t =-2.91,P ＜0.05) after 4 Gy γ-ray irradiation.miRNA microarray revealed that 17 miRNAs were differentially expressed,in which 9 up-regulated,8 down-regulated.The expression levels of miR-124 and miR-34a were coincident with the result of real time RT-PCR.GO analysis showed that some pathways including adherens junction and cell cycle were suppressed,while some immune-related pathways were activated.Conclusions miR-34a and miR-194 were involved in the regulation of acute radiation damage,some other miRNAs including miR-124、miR-382 and miR-92a* also played important roles in radiation process.     

Discovery and characterization of miRNAs in mouse thymus responses to ionizing radiation by deep sequencing

To investigate the potential regulatory roles of microRNA (miRNA) in mouse response to ionizing radiation (IR)-induced thymus injury, miRNA expression profiles of mouse thymus with or without IR were analyzed using deep sequencing technology. Potential target candidates of the identified miRNA were predicted using RNAhybrid and miRanda. Differently expressed miRNA targets functional annotation and pathways were noted using Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and non-redundant (NR) databases. In this study, there were 112 differently expressed miRNAs identified, including 45 known mature and 67 novel miRNAs, which meanwhile contained 77 up-regulated and 35 down-regulated miRNAs. The results of quantitative RT-polymerase chain reaction (qRT-PCR) verification were in agreement with the sequencing analysis. And the target genes of miRNA were annotated. These results revealed the differences of miRNA expression, further extended the biological knowledge and greatly facilitated future studies on the function of miRNA in IR-induced thymus injury.     

14 q32 miRNA基因簇与肝细胞癌的发生发展

肝细胞癌（肝癌,hepatocellular carcinoma ,HCC ）是全球范围内发生率和死亡率较高的恶性肿瘤之一。微小RNA（ microRNA,miRNA）是一类内源性、非编码、高度保守的单链小分子RNA,主要在转录后水平抑制靶基因的表达。有些位置相近的miRNA基因在染色体上成簇排列,在一个多顺反子内形成miRNA基因簇,通常以共表达的形式协同作用。在人类14号染色体长臂端的14q32印迹基因区域约215 kb的基因组范围内,聚集了52个miRNA基因。已有研究发现此miRNA基因簇的异常表达与肝癌的发生发展密切相关。该文概括了14 q32 miRNA基因簇的结构特点,并对其在肝癌发生发展过程中所发挥的作用进行了综述。     

结合基因组分析预测炎症相关miRNA及其靶标

目的：预测炎症相关miRNA及其靶基因。方法：将基因组分析结果和miRNA靶标预测结果融合。结果：通过两种方法所产生数据的叠加,可以挑选出候选的关键miRNA和关键靶基因作为进一步实验研究的线索。结论：将基因组分析与靶标预测相结合可以有效减少假阳性预测结果,缩小实验验证的范围。     

Evaluating the forensic application of 19 target microRNAs as biomarkers in body fluid and tissue identification

RNA‐based body fluid and tissue identification has evolved as a promising and reliable new technique to classify type and source of biological evidence in crime cases. In particular, mRNA‐based approaches are currently on the rise to replace conventional protein‐based methods and are increasingly implemented into forensic casework. However, degradation of these nucleic acid molecules can cause issues on laboratory scale and need to be considered for a credible investigation. For this reason, the analysis of miRNAs using qPCR has been proposed to be a sensitive and specific approach to identify the origin of a biological trace taking advantage of their small size and resistance to degradation. Despite the straightforward workflow of this method, suitable endogenous controls are inevitable when performing real-time PCR to ensure accurate normalization of gene expression data in order to allow a meaningful interpretation. In this regard, we have validated reference genes for a set of forensically relevant body fluids and tissues (blood, saliva, semen, vaginal secretions, menstrual blood and skin) and tested 15 target genes aiming to identify abovementioned sample types. Our data showed that preselected endogenous controls (miR26b, miR92 and miR484) and miR144, initially selected as potential marker for the detection of menstrual blood, were the most stable expressed genes among our set of samples. Normalizing qPCR data with these four validated references revealed that only five miRNA markers are necessary to differentiate between the six different cell types selected in this study. Nevertheless, our observations in the present study indicate that miRNA analysis methods may not provide straightforward data interpretation strategies required for an implementation in forensic casework.     

Characterization of microRNA expression profiles in blood and saliva using the Ion Personal Genome Machine® System (Ion PGM™ System)

MicroRNA (miRNA) expression profiling is gaining interest in the forensic community because the intrinsically short fragment and tissue-specific expression pattern enable miRNAs as a useful biomarker for body fluid identification. Measuring the quantity of miRNAs in forensically relevant body fluids is an important step to screen specific miRNAs for body fluid identification. The recent introduction of massively parallel sequencing (MPS) has the potential for screening miRNA biomarkers at the genome-wide level, which allows both the detection of expression pattern and miRNA sequences. In this study, we employed the Ion Personal Genome Machine^® System (Ion PGM™ System, Thermo Fisher) to characterize the distribution and expression of 2588 human mature miRNAs (miRBase v21) in 5 blood samples and 5 saliva samples. An average of 1,885,000 and 1,356,000 sequence reads were generated in blood and saliva respectively. Based on miRDong, a Perl-based tool developed for semi-automated miRNA distribution designations, and manually ascertained, 6 and 19 miRNAs were identified respectively as potentially blood and saliva-specific biomarkers. Herein, this study describes a complete and reliable miRNA workflow solution based on Ion PGM™ System, starting from efficient RNA extraction, followed by small RNA library construction and sequencing. With this workflow solution and miRDong analysis it will be possible to measure miRNA expression pattern at the genome-wide level in other forensically relevant body fluids.