快速提取棉花蕾期高质量RNA的改良方法

棉花组织中因富含棉酚、多糖和单宁等次生代谢物,RNA难分离,易降解,导致现有RNA快速提取试剂盒提取的棉花RNA产率低、质量差,无法应用于实验操作。针对棉花组织次生代谢物多的特点,以酸酚法为基础,结合RNA吸附柱,通过对幼苗期和蕾期棉花叶片RNA提取,总结出一种快速提取棉花组织RNA的方法。与热硼酸法、酸酚法及试剂盒法相比,所述方法具有步骤少、产率高、质量好等特点,操作简单、整个实验在1h内完成,可开发出提取多糖多酚类生物组织RNA试剂盒。     

高通量组织特异表达谱分析技术

测量基因表达谱是研究动物如何发育和应对刺激的重要途径。基因表达谱实验检测的RNA通常来自多种细胞的混合体。这样的数据具有较低的分辨率,不能区分动物体内不同细胞类型的转录组,而且会偏袒RNA含量占优势的组织以及上调的基因。这个问题可以通过获得特异组织的RNA进行表达谱分析来实现。这十几年来已有多种方法被开发出来获取特异的细胞类型或它们的RNA,并与高通量RNA分析技术结合起来生成各种特异组织或细胞的转录组。本综述将介绍这些方法的基本原理和在大尺度表达谱分析中的应用,并讨论它们各自的优点和局限性。     

siRNA脱靶效应研究进展

RNA干扰过程中,siRNA和mRNA特异结合能够使得靶基因沉默。但研究证实,siRNA可能与非靶基因结合而导致非靶基因沉默,这种现象称为siRNA脱靶效应。多种真核生物中的RNA干扰实验证实了脱靶效应的存在。对脱靶机制的研究发现脱靶可能与模体匹配、结构和长dsRNA等有关,很多新方法被提出来预测脱靶概率和检测脱靶基因。通过利用siRNApool、化学修饰和生物信息学方法能够尽可能地降低脱靶效应,提高RNAi实验的质量。对脱靶效应方面的研究进行了总结论述。     

单细胞RNA测序数据分析方法研究进展

单细胞RNA测序(Single cell RNA sequencing,scRNA-Seq)已经广泛应用于细胞分化、肿瘤微环境及多种疾病病因学研究。目前,由于scRNA-Seq具有低捕获率、高噪声、高变异性等特点,通过优化数据分析方法提高测序结果准确性已经成为测序领域的研究热点。对近年来数据分析过程中利用的数学方法进行了总结,讨论了数据分析的优势及存在的问题,以期为新算法的开发和应用提供参考,逐步提高测序结果的可靠性。     

miRNA与甲基化调控研究进展

mi RNA是基因表达调控重要的调节因子,mi RNA的异常表达可以引起许多疾病的发生。众所周知的原因,DNA甲基化、m RNA甲基化等表观遗传学调控对基因的表达及疾病的发生都有很重要的调控作用,那么mi RNA与DNA甲基化、m RNA甲基化等之间的关系是怎样的?利用甲基化的调控模式进行药物研发是否可行?可否针对mi RNA为靶点开发与甲基化调控相关的药物?目前已经取得了一些有价值的研究成果,本文将结合本课题组的一些研究结果进行总结综述。     

A/U富集片段RNA结合蛋白的固相纯化与鉴定

RNA与细胞靶蛋白结合是RNA发挥其生物学功能的重要基础,因此,分离和鉴定RNA结合蛋白是研究RNA功能的必要步骤．目前,RNA结合蛋白的分离和鉴定方法较多,但各有优缺点．本实验利用可溶性碳二亚胺(EDC)介导的缩合反应,将A/U富集片段RNA共价偶联到固相介质amine M-270上,再用固定化RNA经亲和层析从细胞抽提物中分离纯化RNA结合蛋白,并以SDS-PAGE联合质谱分析和Western blotting等方法鉴定RNA特异性结合蛋白．最后通过荧光原位杂交和共聚焦显微镜证明这些RNA特异性结合蛋白确与RNA在细胞内结合．实践证明这一方法简单、高效、易于掌握．     

RNA化学标记技术

RNA是维持细胞生命活动最重要的基础物质之一,越来越多的证据表明它在细胞的生长发育中起重要的调控作用,成为生命科学中兴起的热点。然而,RNA存在时间短且不稳定的特点,造成RNA研究的困难。RNA的空间分布、转录调控机制以及RNA和其他生物大分子的相互作用都需要有效的标记分析方法。随着化学生物学的发展,越来越多的RNA化学标记技术被开发出来,帮助人们更深入地研究RNA相关功能。该文主要介绍RNA体外标记技术、RNA代谢标记以及RNA邻近相互作用等方面的发展及应用。     

非编码RNA与瘢痕疙瘩的关系及研究进展

瘢痕疙瘩是创伤后胶原纤维异常增生引起的过度纤维化疾病,病理表现主要是成纤维细胞过度增殖和细胞外基质异常沉积。然而,因瘢痕疙瘩发病机制尚不完全明确,且缺乏安全有效的治疗方法和预防策略,因此,迫切需要了解其详细的发病机制进而开发全新且安全有效的治疗方法。近年来,大量研究表明,非编码RNA可通过直接靶向关键基因或间接参与瘢痕疙瘩形成经典信号通路影响成纤维细胞增殖、凋亡、侵袭、迁移以及胶原蛋白的异常沉积,进而调控瘢痕疙瘩的进程,同时有研究发现异常表达的非编码RNA可能为瘢痕疙瘩的治疗提供潜在靶点。该文将总结近年来非编码RNA在瘢痕疙瘩中的研究进展及未来通过干预相关非编码RNA来治疗瘢痕疙瘩的前景及挑战。     

环状RNA研究进展

环状RNA(circRNA)出现在转录后的剪切过程中,单链的RNA分子通过共价结合形成一个环形。高通量测序技术的进步对线性非编码RNA(nocoding linear RNA,NCL)进行了全面的探究,这使得NCL重新走入研究者的视野中,尤其是环状RNA。环状RNA已被证实其丰富,高度表达,和进化保守等特性。一些环状RNA已经被证明能够影响microRNA对基因的调控,可以作为miRNA海绵体,并可能对亲本基因有转录调节的作用,有翻译以及其它的一些功能。并且对一些疾病有着重要的作用,对阿尔兹海默症、糖尿病、缺血性心脏病以及一些癌症都有着调控作用,既可以调节疾病的发展也可以作为一种生物标记物来对疾病进行检测。对环状RNA的形成机制、功能、检测方法、novel环状RNA的鉴定以及疾病相关性进行了总结与概述,并对未来研究进行了展望。     

动植物中RNA结合蛋白的研究进展

RNA结合蛋白(RNA-binding proteins)在转录后基因表达调节中起着重要的作用,它通过和RNA相互作用来调节细胞的功能。RNA结合蛋白参与RNA剪接、多聚腺苷化作用、序列编辑、RNA转运、维持RNA的稳定和降解、细胞内定位和翻译控制等RNA代谢的各个方面。主要介绍了RNA结合蛋白的结构、靶标RNA及RNA结合蛋白在动植物和疾病中的研究。     

MicroRNA functions in animal development and human disease

Five years into the 'small RNA revolution' it is hard not to share in the excitement about the rapidly unravelling biology of microRNAs. Since the discovery of the first microRNA gene, lin-4, in the nematode Caenorhabditis elegans, many more of these short regulatory RNA genes have been identified in flowering plants, worms, flies, fish, frogs and mammals. Currently, about 2% of the known human genes encode microRNAs. MicroRNAs are essential for development and this review will summarise our current knowledge of animal microRNA function. We will also discuss the emerging links of microRNA biology to stem cell research and human disease, in particular cancer.     

MicroRNA在肿瘤发生发展和诊断中作用的研究进展

microRNA是一类由内源基因编码的长度约为18-25个核苷酸的非编码单链RNA分子,可以与靶基因mRNA的3'非编码区结合,通过降解靶m RNA或(和)抑制靶m RNA转录后翻译调节靶蛋白的生成,从而发挥其生物学作用。目前,在人体基因组内发现的microRNA已经超过2500多个,可能调节着人类1/3的基因,在维持正常干细胞功能、调控细胞增殖分化及恶性肿瘤发生过程中均起重要作用。既往的研究表明microRNA与基因之间相互调控的失衡导致肿瘤的发生。从分子水平上研究microRNA与肿瘤发生的关系,检测microRNA与肿瘤相关基因表达情况的改变,分析肿瘤组织和血清中microRNA表达量与肿瘤分型的关系,将有利于肿瘤的病因学研究,早期发现和肿瘤治疗及预后判断。本文主要就microRNA在肿瘤发生发展和诊断中作用的研究进展进行了综述。     

Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach, as they have the advantage of producing just a single functional small RNA, which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. All analyses used transiently expressed transgenes delivered by infiltration of leaves with Agrobacterium tumefacians. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5′-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3′-end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time polymerase chain reaction, is also discussed.     

How the RNA isolation method can affect microRNA microarray results

The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana? microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.     

Direct microRNA detection with universal tagged probe and time-resolved fluorescence technology

microRNAs have emerged as the central player in gene expression regulation and have been considered as potent cancer biomarkers for early disease diagnosis. Direct microRNA detection without amplification and labeling is highly desired. Here we present a rapid, sensitive and selective microRNA detection method based on the base stacking hybridization coupling with time-resolved fluorescence technology. Other than planar microarrays, magnetic beads are used as reaction platforms. In this method, one universal tag is used to report all microRNA targets. Its specificity allows for discrimination between microRNAs differing by a single nucleotide, and between precursor and mature microRNAs. This method also provides a high sensitivity down to 20 fM. Moreover, the full protocol can be completed in about 3 h starting from total RNA.     

Droplet digital PCR,a prospective technological approach to quantitative profiling of microRNA

MicroRNA is a special type of regulatory molecules modulating gene expression. Circulating microRNAs found in blood and other biological body fluids are now considered as potential biomarkers of human pathology. Quantitative changes of particular microRNAs have been recognized in many oncological diseases and other disorders. A recently developed method of droplet digital PCR (ddPCR) possesses a number of advantages making this method the most suitable for verification and validation of perspective microRNA markers of various human pathologies. These advantages include high accuracy and reproducibility of microRNA quantification as well as possibility of direct high-throughput determination of the absolute number of microRNA copies within a wide dynamic range. The present review considers microRNA biogenesis, the origin of circulating microRNAs, and methods used for their quantification. The special technical features of ddPCR, which make this method especially attractive for studying microRNAs as biomarkers of human pathologies and for basic research devoted to aspects of gene regulation by microRNA molecules, are also discussed.