小麦长链非编码RNA的预测及功能分析

生物体有部分基因被转录成RNA,但是不编码相应蛋白质,称为长链非编码RNA(lncRNA)。它们参与基因的表观调控,这一过程对动物、植物的生长发育都有重要作用,但是,目前植物中发现和研究的lncRNA较少。为了研究lncRNA在植物中的功能,本研究建立了基于小麦全长cDNA的lncRNA识别程序。从6162条小麦全长cDNA中发现了231条lncRNAs,并从中鉴定出两个新miRNAs,这表明lncRNAs可以通过形成miRNAs前体基因形成其功能。此外,通过序列富集分析,我们从小麦lncRNAs中鉴定出三个保守的调控元件,结果显示小麦lncRNAs可能通过和其它蛋白质或DNA等分子作用,进而参与小麦生长、发育等过程的调控,这些结果对进一步研究植物体内的lncRNA的功能和作用机制具有重要意义。     

长链非编码RNA-重编码调控因子与肿瘤的研究进展

长链非编码RNA(LncRNA)是一类长度超过200核苷酸且不编码蛋白质的RNA分子。肿瘤基因组学的快速发展使LncRNA在人类肿瘤研究方面的功能更加显著。基因间LncRNA(LincRNA)-重编码调控因子(ROR)作为一种新型LncRNA,其作用机制在结直肠癌、胰腺癌、乳腺癌的发生发展过程中有报道。我们就LincRNA-ROR在肿瘤中的相关调控机制以及在不同肿瘤中的研究现状做简要综述,以便对其有进一步了解。     

植物长链非编码RNA的生物信息学预测与分析研究进展

长链非编码RNA(Long non-coding RNAs,lncRNAs)是一类广泛存在于真核生物中,长度大于200个核苷酸、无蛋白编码功能,具有调控基因转录后表达的RNA转录本。新近研究表明,lncRNA在多种生物途径中起着重要调节作用。生物信息学由生物、数学、计算机科学,统计学等多学科交叉产生,能从全局和系统水平对大数据信息进行深入挖掘与分析。采用生物信息学方法预测与分析lncRNA是当前发现和鉴定植物lncRNA的重要策略之一。本文梳理和总结了近年来采用生物信息学预测植物lncRNA及其靶基因的方法策略,以期为今后深入认知植物lncRNA在植物的生长发育过程、抗逆境胁迫及系统进化等过程中的作用研究提供一定参考。     

植物长链非编码RNA调控发育与胁迫应答的研究进展

长链非编码RNAs（long non-coding RNAs,lncRNAs）是一类长度大于200个核苷酸、缺乏明显开放阅读框、很少或者不具有蛋白编码潜能的内源性RNA。鉴于lncRNAs低表达和低保守性的特点,早期阶段认为其是转录副产物,在生物体内不发挥生物学功能。随着对非编码RNA的深入研究,lncRNAs被认为是一种调控其他类型RNA的重要基因组分,参与发育和胁迫应答生物学过程。本文主要阐述lncRNAs的来源及分类、作用机制、lncRNAs在植物发育和胁迫应答方面的生物学功能,为lncRNAs在作物生产育种中的应用研究提供参考。     

生物节律基因非编码RNA调控机制

节律性的振荡不仅存在于生物节律中枢也存在于外周器官、组织及细胞中,其产生依赖于节律基因的转录、转录后及翻译后水平调控。近几年,生物节律转录后水平调控机制研究成为热点。非编码RNA(ncRNAs)调控组分小RNA(microRNA)与长链非编码RNA(lncRNA)作为参与转录后调控的重要分子,已有研究表明microRNA与lncRNA调控节律基因mRNA与蛋白的相位及振幅。本文概述microRNA与lncRNA参与昼夜节律中枢与外周调控的研究进展,为生物节律转录后调控机制的进一步研究提供参考。     

miRNAs与药物成瘾

药物成瘾是一种慢性复发性脑病,主要表现为不可控制的对药物持续渴求和戒断后的高复吸。目前观点认为,成瘾是中脑腹侧被盖（ventral tegmental area,VTA）到伏隔核（nucleus accumbens,NAc）脑区多巴胺能奖赏通路中神经可塑性发生改变而导致的一种神经精神疾病。基因表达变化在神经可塑性中发挥着重要作用,但成瘾药物导致相关脑区结构和功能改变的机制还不甚清楚。微小RNAs（microRNAs,miRNAs）是一类非编码RNA,主要通过结合靶基因mRNA 3′非翻译区（3′untranslated region,3′UTR）,在转录后水平阻断其翻译成蛋白质或触发其不稳定而降解。越来越多的研究证实,miRNAs参与调节成瘾相关神经可塑性的变化。本文较系统地阐述miRNAs在药物成瘾中的作用研究进展,将为深入阐明药物成瘾的机制以及药物成瘾临床有效干预和诊治提供新思路。     

长链非编码RNA的功能与疾病

长链非编码RNAs（long noncoding RNAs,lncRNAs）是一类长度大于200 nt且不表现出任何蛋白质编码潜能的RNAs,在总非编码RNAs(ncRNA)中占有相当大的比例.对lncRNAs的研究将有助于理解生命体多层次的表达调控网络,并有望为复杂疾病的预测、诊断、和治疗提供新的分子依据.本文在简要介绍lncRNAs的基础上,综合分析了lncRNAs与表观遗传、基因表达调控和疾病发生的关系,以期为进一步的研究提供参考.     

LncRNA作为ceRNA调控肿瘤的发生发展

长链非编码RNA(lncRNA)是长度大于200 bp,不编码蛋白质的内源性RNA分子.近年来的研究表明,lncRNA可以作为一种竞争性内源RNA(competing endogenous RNA,ceRNA)吸附miRNA,参与靶基因的表达调控,从而在肿瘤的发生发展中发挥重要的作用.本文从lncRNA作为ceRNA发挥生物学功能这一角度,概述了相关lncRNA在肿瘤发生发展中的作用及机制.揭秘lncRNA与miRNA在肿瘤发生中的相互作用,将为肿瘤的诊断和治疗提供新思路.     

lncRNAs功能注释和预测

随着测序技术的发展,在各种哺乳动物中发现越来越多的长非编码RNAs（long non-coding RNAs,lncRNAs）,但是大部分lncRNAs的功能却未知.鉴于lncRNAs在众多生物过程如免疫反应、发育和基因印迹中表现出对蛋白编码基因和其它非编码RNAs的重要调节作用,对lncRNAs的功能研究也成为生物学家和生物信息学家研究的热点. 其中,功能注释和预测是目前研究lncRNAs功能的主要方法之一.本文主要对lncRNAs功能注释和预测方法的研究进展作一综述,包括以下几个方面：基于共表达网络的方法、基于miRNAs的方法、基于蛋白质结合的方法、基于表观遗传修饰的方法以及基于ceRNA网络的方法. 为进一步研究lncRNAs的功能提供参考,同时为开发更加有效的注释或预测方法提供线索.     

综述: 新型长链非编码RNA(lncRNA)的生物信息学研究进展

非编码RNA (noncoding RNA,ncRNA)是指不被翻译成蛋白质的一类RNA,近几年来关于它们的功能研究越来越引起人们的重视．现在已经发现了一些中小型ncRNA,比如microRNA、snoRNA、tRNA等,但是关于长ncRNA(lncRNA)的研究还不够完善．本篇综述回顾了 ncRNA特别是 lncRNA的生物信息学研究进展,包括它们的研究历程、基本特点、与疾病的关系,以及对已有的预测非编码RNA的计算机方法进行了分析和比较,并且介绍了利用机器学习模型整合新一代高通量测序数据的方法．     

EBV编码miRNAs在病毒感染和肿瘤发生中的功能和意义

EB病毒(Epstein-Barr virus,EBV)是一种172 kb大小的线性双链DNA病毒,与鼻咽癌、淋巴瘤、胃癌等恶性肿瘤的发生密切相关. EBV编码的微小RNAs (miRNAs)可以调节病毒和宿主细胞基因的表达,并且在癌症发生发展中起着多种作用.本文综述了EBV编码的miRNAs (EBV-encoded miRNA,EBV miRNAs)在病毒感染和肿瘤发生、侵袭转移、抗凋亡、信号通路等方面的生物学功能,以及对于EBV相关肿瘤诊断标志物的潜在意义. EB病毒编码的miRNAs也可能成为进一步研究EBV相关肿瘤治疗的一个候选靶点.     

LINC01101 and LINC00277 expression levels as novel factors in HPV‐induced cervical neoplasia

Recently long non‐coding RNAs were identified as new factors involved in gene expression regulation. To gain insight into expression pattern of these factors related to E7 HPV18 oncogene, this study uses HeLa cell culture transfected with E7‐siRNA. Gene expression profile was investigated using microarray analysis. After analysing the microarray results, we identified 15,387 RNA species differentially expressed in E7‐siRNA‐transfected cells compared with controls (fold change >2). The expression profiles of lncRNA species highlighted 731 lncRNAs and 203 lincRNAs. We selected two lincRNAs (LINC01101 and LINC00277) and we evaluated the expression profile in HPV‐induced neoplasia. Both lincRNAs investigated display a significantly reduced pattern of expression in cervical lesions and cancer, associated with clinical parameters. A connection between HPV presence and lincRNAs was noted. hrHPV‐positive samples exhibit significantly reduced LINC01101 and LINC00277 expression level (P < 0.05). These results provide new insights into involvement of lncRNA in HPV‐induced cervical cancer, enriching our understanding of their potential role in this pathology.     

小细胞外囊泡及其携带的非编码RNA在非酒精性脂肪性肝病中的作用

小细胞外囊泡（small extracellular vesicles,sEVs）是由细胞分泌的一种细胞外囊泡,产生于多泡体,多泡体与质膜融合并释放到细胞外基质。由于小细胞外囊泡可以携带分子质量相对较小的核酸、蛋白质、脂质,能够执行细胞间物质传递、细胞间通讯等功能。因此,小细胞外囊泡及其携带的非编码RNA不仅参与细胞正常生理过程,也可以在多种疾病的发生发展过程中起重要作用。本文综述了小细胞外囊泡在非酒精性脂肪性肝病（NAFLD）中的作用,小细胞外囊泡及其携带的非编码RNA不仅有望成为NAFLD诊断的标志物,同时也具有治疗NAFLD的潜在作用,或能为治疗NAFLD提供新思路。     

Exosomes and their importance in metastasis,diagnosis, and therapy of colorectal cancer

Extracellular vesicles are known as actual intermediaries of intercellular communications, such as biological signals and cargo transfer between different cells. A variety of cells release the exosomes as nanovesicular bodies. Exosomes contain different compounds such as several types of nucleic acids and proteins. In this study, we focused on exosomes in colorectal cancer as good tools that can be involved in various cancer-related processes. Furthermore, we summarize the advantages and disadvantages of exosome extraction methods and review related studies on the role of exosomes in colorectal cancer. Finally, we focus on reports available on relations between mesenchymal stem cell–derived exosomes and colorectal cancer. Several cancer-related processes such as cancer progression, metastasis, and drug resistance of colorectal cancer are related to the cargoes of exosomes. A variety of molecules, especially proteins, microRNAs, and long noncoding RNAs, play important roles in these processes. The microenvironment features, such as hypoxia, also have very important effects on the properties of the origin cell–derived exosomes. On the other hand, exosomes derived from colorectal cancer cells also interfere with cancer chemoresistance. Furthermore, today it is known that exosomes and their contents can likely be very effective in noninvasive colorectal cancer diagnosis and therapy. Thus, exosomes, and especially their cargoes, play different key roles in various aspects of basic and clinical research related to both progression and therapy of colorectal cancer.     

Profiling the circulating miRNAs in mice exposed to gram-positive and gram-negative bacteria by Illumina small RNA deep sequencing

Background

We profiled the expression of circulating microRNAs (miRNAs) in mice using Illumina small RNA deep sequencing in order to identify the miRNAs that may potentially be used as biomarkers to distinguish between gram-negative and gram-positive bacterial infections.

Results

Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) were used to induce bacterial infection in mice at a concentration of 1 × 10⁸ bacteria/100 μL of phosphate buffered saline (PBS). Small RNA libraries generated from the serum of mice after exposure to PBS, Xen14, Xen29, and Xen14 + Xen29 via the routes of subcutaneous injection (I), cut wound (C), or under grafted skin (S) were analyzed using an Illumina HiSeq2000 Sequencer. Following exposure to gram-negative bacteria alone, no differentially expressed miRNA was found in the injection, cut, or skin graft models. Exposure to mixed bacteria induced a similar expression pattern of the circulating miRNAs to that induced by gram-positive bacterial infection. Upon gram-positive bacterial infection, 9 miRNAs (mir-193b-3p, mir-133a-1-3p, mir-133a-2-3p, mir-133a-1-5p, mir-133b-3p, mir-434-3p, mir-127-3p, mir-676-3p, mir-215-5p) showed upregulation greater than 4-fold with a p-value < 0.01. Among them, mir-193b-3p, mir-133a-1-3p, and mir-133a-2-3p presented the most common miRNA targets expressed in the mice exposed to gram-positive bacterial infection.

Conclusions

This study identified mir-193b-3p, mir-133a-1-3p, and mir-133a-2-3p as potential circulating miRNAs for gram-positive bacterial infections.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-014-0106-y) contains supplementary material, which is available to authorized users.     

Identification of functional lncRNAs in atrial fibrillation by integrative analysis of the lncRNA-mRNA network based on competing endogenous RNAs hypothesis

A mounting body of evidence has suggested that long noncoding RNAs (lncRNAs) play critical roles in human diseases by acting as competing endogenous RNAs (ceRNAs). However, the functions and ceRNA mechanisms of lncRNAs in atrial fibrillation (AF) remain to date unclear. In this study, we constructed an AF-related lncRNA-mRNA network (AFLMN) based on ceRNA theory, by integrating probe reannotation pipeline and microRNA (miRNA)-target regulatory interactions. Two lncRNAs with central topological properties in the AFLMN were first obtained. By using bidirectional hierarchical clustering, we identified two modules containing four lncRNAs, which were significantly enriched in many known pathways of AF. To elucidate the ceRNA interactions in certain disease or normal condition, the dysregulated lncRNA-mRNA crosstalks in AF were further analyzed, and six hub lncRNAs were obtained from the network. Furthermore, random walk analysis of the AFLMN suggested that lncRNA RP11-296O14.3 may function importantly in the pathological process of AF. All these eight lncRNAs that were identified from previous steps (RP11-363E7.4, GAS5, RP11-410L14.2, HAGLR, RP11-421L21.3, RP11-111K18.2, HOTAIRM1, and RP11-296O14.3) exhibited a strong diagnostic power for AF. The results of our study provide new insights into the functional roles and regulatory mechanisms of lncRNAs in AF, and facilitate the discovery of novel diagnostic biomarkers or therapeutic targets.     

茄子microRNAs与其靶基因的生物信息学预测

microRNAs(miRNAs)是一类在真核生物中发现的长度为21 nt左右、非编码、内源性的单链小分子RNA,通过与靶基因的互补发挥转录后水平的负调控作用。目前,已在许多物种中报道了miRNAs的存在,然而还未见关于茄子miRNAs的报道。根据miRNAs在植物中的高度保守性及其前体的二级结构特征,文章通过同源预测的方法,将已知植物的miRNAs与茄子EST数据库比对,经过一系列的筛选,最终预测到12个家族的16条茄子miRNAs,其中包括3个miRNA家族的正义/反义miRNAs,而miR390和miR399家族的正义/反义miRNAs属于第一次发现。文章还通过在线软件psRNATarget预测到15条茄子miRNAs的71个靶基因,这些靶基因主要编码与茄子生长发育、新陈代谢以及胁迫响应等过程相关的蛋白。