Molecular mechanisms underlying roles of long non-coding RNA small nucleolar RNA host gene 16 in digestive system cancers

This editorial reviews the molecular mechanisms underlying the roles of the long non-coding RNA(lncRNA)small nucleolar RNA host gene 16(SNHG16)in digestive system cancers based on two recent studies on lncRNAs in digestive system tumors.The first study,by Zhao et al,explored how hBD-1 affects colon cancer,via the lncRNA TCONS_00014506,by inhibiting mTOR and promoting autophagy.The second one,by Li et al,identified the lncRNA prion protein testis specific(PRNT)as a factor in oxaliplatin resistance by sponging ZNF184 to regulate HIPK2 and influence colorectal cancer progression and chemoresistance,suggesting PRNT as a potential therapeutic target for colorectal cancer.Both of these two articles discuss the mechanisms by which lncRNAs contribute to the development and progression of digestive system cancers.As a recent research hotspot,SNHG16 is a typical lncRNA that has been extensively studied for its association with digestive system cancers.The prevailing hypothesis is that SNHG16 participates in the development and progression of digestive system tumors by acting as a competing endogenous RNA,interacting with other proteins,regulating various genes,and affecting downstream target molecules.This review systematically examines the recently reported biological functions,related molecular mechanisms,and potential clinical significance of SNHG16 in various digestive system cancers,and explores the relationship between SNHG16 and digestive system cancers.The findings suggest that SNHG16 may serve as a potential biomarker and therapeutic target for human digestive system cancers.

细菌sRNA来源、作用机制及调控网络研究进展

通过发酵生产工业产品一直是细菌等微生物的研究热点,但是发酵过程中存在的代谢副产物和环境胁迫等问题,限制了工业菌株的发展。sRNA是细菌中普遍存在的一类调控性非编码RNA,它们与核糖开关、双组分系统、转录因子等其他调控元件共同构成了细菌中的复杂调控网络,在代谢调控和抗胁迫中都发挥着异常重要的作用。文章对细菌中sRNA的来源、作用机制以及在调控网络中的角色进行了详细总结,有助于更好地解析细菌的代谢途径及发酵过程中受到的环境限制,对构建低毒力、高鲁棒性菌株,助力工业产品的发酵生产有重要参考意义。

Small regulators making big impacts:regulation of neural stem cells by small non-coding RNAs

Neurodegeneration and traumatic brain injuries are leading causes of disability and present an enormous disease burden both in terms of patient suffering and healthcare cost.Treatment of brain lesions remains as a major challenge in medicine largely because of the limited regenerative capacity of the adult brain.

Prediction of candidate small non-coding RNAs inAgrobacterium by computational analysis

Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.

Non-coding RNAs and gastric cancer

Non-coding RNAs(ncRNAs)play key roles in development,proliferation,differentiation and apoptosis.Altered ncRNA expression is associated with gastric cancer occurrence,invasion,and metastasis.Moreover,aberrant expression of microRNAs(miRNAs)is significantly related to gastric cancer tumor stage,size,differentiation and metastasis.MiRNAs interrupt cellular signaling pathways,inhibit the activity of tumor suppressor genes,and affect the cell cycle in gastric cancer cells.Some miRNAs,including miR-21,miR-106a and miR-421,could be potential markers for the diagnosis of gastric cancer.Long non-coding RNAs (lncRNAs),a new research hotspot among cancerassociated ncRNAs,play important roles in epigenetic,transcriptional and post-transcriptional regulation.Several gastric cancer-associated lncRNAs,such as CCAT1,GACAT1,H19,and SUMO1P3,have been explored.In addition,Piwi-interacting RNAs,another type of small ncRNA that is recognized by gastroenterologists,are involved in gastric carcinogenesis,and piR-651/823represents an efficient diagnostic biomarker of gastric cancer that can be detected in the blood and gastric juice.Small interfering RNAs also function in posttranscriptional regulation in gastric cancer and might be useful in gastric cancer treatment.

Targeting long non-coding RNA MALAT1 alleviates retinal neurodegeneration in diabetic mice

●AIM:To observe the effect of inhibiting long non-coding RNA(lncRNA)metastasis-associated lung adenocarcinoma transcript 1(MALAT1)on diabetic neurodegeneration.●METHODS:Thirty-six 8-week-old C57 BL/6 mice were randomly divided into normal control,diabetic control,diabetic scrambled small interfering RNAs(siRNAs)and diabetic MALAT1-siRNA groups.After diabetic induction with streptozocin intraperitoneally-injection,the diabetic M A L AT 1-s i R N A g ro u p w a s i n t r av i t r e a l l y i n j e c te d with 1μL 20μmol/L MALAT1 siRNA,and the diabetic scrambled siRNA group was injected with the same amount of scrambled siRNA.Electroretinography was performed to examine photoreceptor functions 16 wk after diabetes induction.MALAT1 expression was detected via real time polymerase chain reaction.Cone morphological changes were examined using immunofluorescence.Rod morphological changes were examined by determining outer nuclear layer(ONL)thickness.●RESULTS:The upregulation of retinal MALAT1 expression was detected in the diabetic control mice,while MALAT1 expression in the diabetic MALAT1-siRNA mice was decreased by 91.48%compared to diabetic control mice.The diabetic MALAT1-siRNA and diabetic control mice showed lower a-wave and b-wave amplitudes than did the normal control mice in scotopic and photopic electroretinogram,while the diabetic MALAT1-siRNA mice showed higher amplitudes than diabetic control mice.Morphological examination revealed that ONL thickness in the diabetic MALAT1-siRNA and diabetic control mice was lower than normal control mice.However,ONL thickness was greater in the diabetic MALAT1-siRNA mice than diabetic control mice.Moreover,the diabetic control mice performed a sparser cone cell arrangement and shorter outer segment morphology than diabetic MALAT1-siRNA mice.●CONCLUSION:Inhibiting retinal MALAT1 results in mitigative effects on the retinal photoreceptors,thus alleviating diabetic neurodegeneration.

细菌中糖转运相关sRNA 的生理调控功能

当细菌面对较高浓度的葡萄糖时,随着葡萄糖摄入,常会导致菌体内部葡糖-6-磷酸的大量累积。在磷酸糖浓度达到一定阈值时,就会形成一种毒性胁迫从而抑制菌体的代谢与生长。许多细菌则会通过一种小RNA SgrS (sugar transport-related sRNA)的转录后调控作用,来解除这种糖胁迫抑制作用。SgrS在分子伴侣Hfq的协助下,与相应靶mRNA通过碱基互补配对方式结合,对ptsG mRNA和manXYZ mRNA进行负调控以减少糖类摄入,并对yigL mRNA进行正调控以增大糖类排出,从而提高细胞对糖胁迫的耐受性。与一般sRNA不同,SgrS作为一种双功能sRNA,除具有转录后调控功能外,还能够翻译出蛋白质SgrT。SgrS广泛存在于肠杆菌中,但不同菌属中SgrS的差异极大。本文主要对SgrS在细菌中的功能、分布及其差异进行综述。

细菌sRNA数据库

细菌sRNA是一类长度在50~500 nt的调控小RNA(small regulatory RNA),主要通过与靶标mRNA或靶标蛋白质结合发挥多种生物学功能。目前,随着生物信息学与高通量测序的应用,发现了越来越多的细菌sRNA,开发了多个相关数据库。为了sRNA工作者系统了解与应用这些数据,本文拟对包含细菌sRNA的综合数据库和细菌sRNA专业数据库作一概述,并对sRNA数据库的未来发展进行展望。

Novel aspects of tRNA-derived small RNAs with potential impact in infectious diseases

The complete understanding of the growing catalog of regulatory non-coding RNAs is going to shed light in different aspects of a wide range of pathogenic mechanisms in human diseases. This review was aimed to highlight recent advances in the small non- coding RNA world that could have implications in the development of new strategies in medical sciences. Among the diverse group of small non-coding RNAs, we highlight the group of tRNA-derived fragments as molecules known for a long time which have recently emerged as novel regulators influencing several aspects of cell biology. We describe here recent advances in the field of tRNA-derived fragments playing key roles in the biology of some infectious agents, including E. coli, A. fumigatus, G. lamblia, Ascaris, T. cruzi, Virus, Prions and a brief overview linking them to cancer biology. Additionally, we focus on the potential implications of these molecules in future biotechnological applications in the development of new biomarkers and as new therapeutic targets.

细菌sRNA调控靶标的双质粒筛选系统构建

以pMycVec1/pMycVec2载体为基础,构建了筛选和鉴定细菌sRNA调控靶标的双质粒系统。对pMycVec2载体的多克隆位点进行改造,并加入强启动子rrnBp和有效转录终止子,获得可定向克隆和转录sRNA的质粒pMycVec2-D;对pMycVec1载体的多克隆位点进行改造,并加入弱启动子Pwk和有效转录终止子,获得了分别用报告基因lacZ和GFP来检测sRNA靶标序列翻译水平的质粒pMycVec1-lacZ和pMycVec1-GFP。最后,利用2对已知的sRNA与其调控靶标MicC/ompC mRNA和MicF/ompF mRNA,通过β-半乳糖苷酶活性和菌体荧光值检测,表明双质粒系统能有效检测sRNA与调控靶标的互作。

Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain

Dunaliella salina is a classic halophilic alga.However,its molecular mechanisms in response to high salinity at the post transcriptional level remain unknown.A unique halophilic alga strain,DS-CN1,was screened from four D.salina strains via cell biological,physiological,and biochemical methods.High-throughput sequencing of small RNAs(sRNAs)of DS-CN1 in culture medium containing 3.42-mol/L NaCl(SS group)or 0.05-mol/L NaCl(CO group)was performed on the BGISEQ-500 platform.The annotation and sequences of D.salina sRNAs were profiled.Altogether,44 novel salt stress-responsive microRNAs(miRNAs)with a relatively high C content,with the majority of them being 24 nt in length,were identified and characterized in DS-CN1.Twenty-one differentially expressed miRNAs(DEMs)in SS and CO were screened via bioinformatic analysis.A total of 319 putative salt stress-related genes targeted(104 overlapping genes)by novel miRNAs in this alga were screened based on our previous transcriptome sequencing research.Furthermore,these target genes were classified and enriched by GO and KEGG pathway analysis.Moreover,5 novel DEMs(dsa-mir3,dsa-mir16,dsa-mir17,and dsa-mir26 were significantly upregulated,and dsa-mir40 was significantly downregulated)and their corresponding 10 target genes involved in the 6 significantly enriched metabolic pathways were verified by quantitative real-time PCR.Next,their regulatory relationships were comprehensively analyzed.Lastly,a unique salt stress response metabolic network was constructed based on the novel DEM-target gene pairs.Taken together,our results suggest that 44 novel salt stress-responsive microRNAs were identified,and 4 of them might play important roles in D.salina upon salinity stress and contribute to clarify its distinctive halophilic feature.Our study will shed light on the regulatory mechanisms of salt stress responses.

大鼠软骨生成过程表达的小分子RNA生物信息学分析

目的：分析大鼠软骨形成过程中小分子 RNA（sRNA）表达谱变化及其基因功能,探讨软骨细胞增殖与分化的机制。方法取新生、断乳、性成熟3个时间节点的雌性 SD 大鼠股骨头软骨构建 sRNA 文库,Solexa 测序平台鉴定软骨组织全部 sRNA 序列表达,所得的全部清洁序列与 SD 大鼠基因组信息比对,并做生物信息学分析。结果3个文库筛选出与基因组序列完全匹配序列,分别对应着217921条（41.23%）、196650条（38.74%）、245436条（41.54%）unique sRNA 序列。长度为20~24 nt 的 sRNA 占比：d 0为71.94%、d 21为72.85%、d 42为86.39%；其中,长度为22 nt的 sRNA 约占清洁序列的一半。文库序列分布特征,符合高质量 sRNA 文库的特征。超过总数62%的清洁序列来自于成熟 miRNA 序列,但在3个文库中的占比却仅仅只有0.69%、0.78%和0.63%。约60%的unique sRNA 序列无法与 miRBase 20.0和 Rfam9.1匹配。结论3个 sRNA 文库的 miRNA 这种分布模式,可能暗示着有功能不同或者来源各异的 miRNA,参与了对骨骼发育和骨形成关键阶段软骨细胞增殖与分化的调控。

细菌非编码小RNA的研究与展望

细菌非编码小RNA（sRNA）是近年来在原核生物体内发现的长度在40∽500 bp的RNA。sRNA在基因组中被转录,但自身不能编码蛋白质,一般需要Hfq协助,在转录后水平与mRNA结合,影响mRNA的稳定性和翻译,从而调控生命活动,是细菌代谢、群体感应、适应环境、应激反应及毒力基因表达的重要调节因子。目前,各类细菌中发现的sRNA超过150种,研究方法主要有传统的实验室检测分析法和基于生物信息学的预测法。

A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa

Accumulating evidence suggests that non-coding RNAs （ncRNAs） are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5＇ and 3＇ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs （snoRNAs） were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGOlb in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.

Global Analysis of Non-coding Small RNAs in Arabidopsis in Response to Jasmonate Treatment by Deep Sequencing Technology

In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.

跨界小RNA参与植物病原菌互作的研究进展

植物小RNA介导的RNA干扰在植物响应病原菌侵染的免疫反应中发挥重要作用。研究发现,小RNA(sRNAs)可以跨界转运,参与植物免疫和病原菌的致病过程,这种突破物种界限,转运到寄主或微生物体内沉默靶基因的现象,称为跨界RNA干扰(Cross-kingdom RNAi)。跨界RNA干扰技术的应用为当前植物保护和抗病育种提供了新的方向。文章综述了跨界sRNAs的合成路径、转运机制及其在植物免疫和病原菌毒力方面的研究进展,以期为跨界RNA干扰技术在植物病害防控领域的应用提供参考信息。

The biogenesis and biological roles of tRNA-derived short RNAs

In recent years, next-generation sequencing (NGS) technologies targeting the microRNA (miRNA)transcriptome revealed the existence of tRNA-derived short RNAs: tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs). These small RNAs represent a novel type of small non-coding RNAs (sncRNAs), which are heterogeneous in size, nucleotide composition and biogenesis, and have been suggested to be involved in translation, cell proliferation, priming of viral reverse transcriptases, regulation of gene expression, modulation of the DNA damage response, tumor suppression and neurological disorders. Herein, we review the mechanism of their biogenesis and discuss in detail the regulatory roles they play in cell physiology. We also point out that the biological function of tRNA-derived short RNAs will be understood better as research moves forward, and that this knowledge will find its way into clinical application in the near future.

链球菌非编码小RNA研究进展

非编码小RNA(Small non-coding RNA,sRNA)是一种存在于原核和真核生物中的新型调控RNA,长度约为40~500个核苷酸。作为一类关键的调控因子,sRNA通过与靶mRNA或蛋白质结合来调控细胞内的基因表达。大部分细菌sRNA在大肠杆菌等革兰氏阴性菌中被发现并研究,但近十年来越来越多的sRNA在革兰氏阳性菌中被逐步发现。作为一类革兰氏阳性菌,链球菌属中sRNA目前研究主要集中在毒力调节,鲜有其他调控的报道。本文总结了链球菌中sRNA的最新进展,并介绍其主要功能和机理,以期为细菌sRNA研究提供借鉴。

谷氨酸棒杆菌不同生长时期非编码sRNA的预测与鉴定

【目的】探究与挖掘不同生长时期谷氨酸棒杆菌(Corynebacterium glutamicum)中潜在的小的非编码RNA(small non-coding RNA,sRNA)。【方法】检测不同时期和不同工业改造的谷氨酸棒杆菌菌株的RNA-Seq数据构建表达文库,通过sRNA-Detect和APERO两种方法构建潜在的sRNA数据库。以逆转录PCR检测(real-time reverse transcription PCR,RT-PCR)方法检测sRNA的表达,并通过生物信息学方法分析潜在sRNA的调控位点、二级结构及保守结构域。【结果】构建了包含2653条潜在sRNA的数据库,依据其相较于编码序列(coding sequence,CDS)区域的位置进行分类、预测功能。发现了在高GC革兰氏阳性菌中普遍存在的sRNA00130,随生长时期表达量变化的sRNA00257,常时高表达的sRNA02036、sRNA02037等sRNA。依据自由结合能预测潜在sRNA可能的结合位点、二级结构,预测结果显示潜在的sRNAs同多种细胞复制、代谢通路基因相关。大多数潜在sRNA仅在谷氨酸棒杆菌中具有保守性。【结论】谷氨酸棒杆菌潜在sRNA的发掘对于填补谷氨酸棒杆菌生长调控机制的空缺具有重要作用,提供了新的可能的调控工具与改造位点。

Long Non-coding RNAs and Their Biological Roles in Plants

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non- protein-coding RNAs （npcRNAs or ncRNAs）. Among them, long npcRNAs or ncRNAs 0npcRNAs or lncRNAs） represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in olants.