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．     

Primate-specific Long Non-coding RNAs and MicroRNAs

Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics. Here, we have summarized the studies regarding regulatory roles of some key primate-specific lncRNAs and miRNAs.     

Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response

Abiotic and biotic stressors in human cells are often a result of sudden and/or frequent changes in environmental factors. The molecular response to stress involves elaborate modulation of gene expression and is of homeostatic, ecological, and evolutionary importance. Although attention has primarily focused on signaling pathways and protein networks, long non-coding RNAs (ncRNAs) are increasingly involved in the molecular mechanisms associated with responses to cellular stresses. We identified six novel short-lived long ncRNAs (MIR22HG, GABPB-AS1, LINC00152, IDI2-AS1, SNHG15, and FLJ33630) that responded to chemical stressors (cisplatin, cycloheximide, and mercury (II) oxide) in HeLa Tet-off cells. Our results indicate that short-lived long ncRNAs respond to general and specific chemical stressors. The expression levels of the short-lived long ncRNAs were elevated because of prolonged decay rates in response to chemical stressors and interruption of RNA degradation pathways. We propose that these long ncRNAs have the potential to be surrogate indicators of cellular stress responses.     

Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures

The secondary structure is a fundamental feature of both non-coding RNAs (ncRNAs) and messenger RNAs (mRNAs). However, our understanding of the secondary structures of mRNAs, especially those of the coding regions, remains elusive, likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure like those binding to ncRNAs. Indeed, mRNAs have recently been found to adopt diverse alternative structures, but the overall functional significance remains untested. We hereby approach this problem by estimating the folding specificity, i.e., the probability that a fragment of an mRNA folds back to the same partner once refolded. We show that the folding specificity of mRNAs is lower than that of ncRNAs and exhibits moderate evolutionary conservation. Notably, we find that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding. Our findings reveal a novel facet of the RNA structurome with important functional and evolutionary implications and indicate a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.     

Small regulatory non‐coding RNAs in bacteria: physiology and mechanistic aspects

Regulatory ncRNAs (non‐coding RNAs) adjust bacterial physiology in response to environmental cues. ncRNAs can base‐pair to mRNAs and change their translation efficiency and/or their stability, or they can bind to proteins and modulate their activity. ncRNAs have been discovered in several species throughout the bacterial kingdom. This review illustrates the diversity of physiological processes and molecular mechanisms where ncRNAs are key regulators.     

地中海富盐菌中非编码RNA的鉴定与分析

【目的】通过转录组高通量测序技术(即RNA-seq),结合生物信息学分析和分子生物学方法,在组学水平鉴定极端嗜盐菌中可能的非编码RNA(nc RNA)。【方法】将培养至对数中期的地中海富盐菌在不同盐浓度下处理30分钟,提取RNA,进行链特异的转录组测序和5′端区分的转录组测序,通过生物信息学分析在全基因组范围内鉴定nc RNA,预测其转录边界;然后通过Northern blot和环化RNA反转录聚合酶链式反应(CR-RT-PCR)对部分预测的nc RNA进行实验验证。【结果】比较两种RNA-seq技术在不同培养条件下的RNA测序结果和对转录单元的精细分析,共鉴定到105个高可信度的nc RNA,并发现4个在不同盐度下表达差异较大的nc RNA,通过Northern blot和CR-RT-PCR验证了inc RNA1436和inc RNA1903的表达情况、转录本、转录起始位点及终止位点等。【结论】首次在组学水平鉴定了地中海富盐菌中的nc RNA,不同盐浓度刺激下部分nc RNA的转录差异暗示其有可能参与地中海富盐菌对盐胁迫的适应,高可信度nc RNA的组学发现为今后全面开展嗜盐古菌nc RNA的功能机制研究提供了基础数据及重要的切入点。     

RNA结合蛋白与非编码RNA调节关系的研究进展

近年来,越来越多的研究表明,RNA结合蛋白(RNA binding protein,RBP)与多种类型的非编码RNAs(noncoding RNA,ncRNAs)具有互相调节的关系,且调节机制形式多样。一方面,RBP可以调节ncRNA的生物合成、稳定性和功能;另一方面,ncRNA也可以影响RBP的功能和结构。同时,RBP和ncRNA的相互作用还在其他靶基因的调节上起着重要的作用,从而参与众多的生物过程,如组织发育、代谢性疾病、神经退行性疾病、抗病毒免疫和各种癌症等。该文就RBP与常见类型的ncRNAs,包括miRNA、lncRNA、circRNA的相互作用方式和调节机制的研究进展作一综述。     

Genetic regulation by non-coding RNAs

Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs’ past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs.     

Genetic regulation by non-coding RNAs

Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs' past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs.     

非编码RNAs在细菌代谢网络调控中的研究进展

非编码RNAs(non-coding RNAs,ncRNAs)是一类非常重要的调节子,此类调节子能够使细胞通过调节它们的生理特性而适应环境的改变。已有的研究表明ncRNAs在细菌的蔗糖代谢、细胞外膜应激反应、群体感应和细菌毒力等方面发挥了重要的调节作用,其调控模式已经成为细菌调控网络中的重要“分支”。本文综述了细菌ncRNAs近年来的研究进展,详细介绍了细菌ncRNAs的合成及调控机制,由于ncRNAs结构的独特性及调控网络的复杂性,因此ncRNAs的功能研究已经成为近几点的研究热点之一。     

Non‐coding RNA involvement in the pathogenesis of diabetic cardiomyopathy

In recent years, the incidence of diabetes has been increasing rapidly, which seriously endangers human health. Diabetic cardiomyopathy, an important cardiovascular complication of diabetes, is characterized by myocardial fibrosis, ventricular remodelling and cardiac dysfunction. It has been documented that mitochondrial dysfunction, oxidative stress, inflammatory response, autophagy, apoptosis, diabetic microangiopathy and myocardial fibrosis are implicated in the pathogenesis of diabetic cardiomyopathy. With the development of molecular biology technology, accumulating evidence demonstrates that non‐coding RNAs (ncRNAs) are critically involved in the molecular mechanisms of diabetic cardiomyopathy. In this review, we summarize the pathological roles of three types of ncRNAs (microRNA, long ncRNA and circular RNA) in the progression of diabetic cardiomyopathy, which may provide valuable insights into the pathogenesis of diabetic cardiovascular complications.     

河蟹螺原体非编码RNA及其毒力靶标的多组学系统挖掘*

我国是世界最大水产养殖国,每年甲壳动物因病害造成的经济损失约为70亿元。其中,螺原体(Spiroplasma)是甲壳动物重要的致病菌之一,可造成虾蟹大面积死亡,已列入农业农村部三类疫病。非编码RNA(ncRNA)广泛存在于细菌中,其主要通过碱基配对识别靶标mRNA在转录后水平调节基因的表达,部分ncRNAs通过与蛋白质相互作用而影响蛋白质功能。近年研究表明,细菌ncRNAs在毒力调控中扮演极为重要的角色。为了研究河蟹螺原体ncRNAs在甲壳动物致病中的分子调控作用,需系统筛选鉴定螺原体感染相关的ncRNAs和毒力靶标。通过比较基因组、差异转录组、定量蛋白质组、系统生物学和分子相互作用联合研究得到:整合基因组和转录组挖掘得到河蟹螺原体ncRNAs 共54个;在体内感染和体外培养的不同时期,利用数字基因表达谱分析分别得到11个和28个差异显著ncRNAs;利用4款生物软件预测ncRNAs靶标,取交集得到423个;利用定量蛋白质组检测,鉴定出68个差异毒力蛋白,这些差异毒力蛋白与ncRNAs的30个毒力靶标中的21个相同;利用网络生物学分析得到主要的节点Hub-ncRNA共有6个;利用RNA pull-down、原核链特异性测序和LC-MS/MS综合分析,得到重要节点ncRNA SR05的互作RNA 53个、互作蛋白质120个。相关研究成果,可为诠释河蟹螺原体致病机制及其与宿主相互作用机制奠定基础,为虾蟹该疾病的综合防治提供科学依据。