梨花芽休眠相关miRNA的鉴定和差异表达分析

为了探究梨花芽休眠进程中miRNA的表达模式和靶基因,利用Solexa测序技术、生物信息学分析和实时荧光定量PCR（qPCR）技术,对内休眠、内休眠解除和生态休眠解除3个时期梨花芽的miRNA进行高通量测序、筛选和鉴定。结果表明,内休眠、内休眠解除和生态休眠解除时期3个样本文库中分别有12 276 226、10 135 952、11 453 981条Unique序列。miRNA主要分布在21 ~ 24 nt之间,其中长度为24 nt的数量最多。共检测到151个已知的miRNA,属于39个不同的家族,并利用生物信息学软件预测到了209个新的miRNAs。比较分析从内休眠进入到生态休眠解除的整个休眠转换时期差异表达的miRNA,筛选出8个miRNA（ahy-miR156b-5p、cpa-miR319、aly-miR172c-3p、aau-miR396、mdm-miR858、aly-miR171b-3p、bdi-miR160f和hbr-miR166a）,其靶基因主要参与转录调控、信号传导等过程。利用qPCR验证了8个miRNA及其8个靶基因的表达。     

MiRNAs在番茄钾营养胁迫中的作用

以低钾不同耐性的2种基因型番茄(JZ18-钾敏感型和JZ34-耐低钾型)为试材,采用新一代高通量测序技术,对低钾胁迫下2种不同基因型番茄根系miRNAs进行测序,根据检测结果进行生物信息学分析,以期为研究响应低钾胁迫的关键miRNA提供参考依据。结果表明:低钾胁迫下,2个基因型番茄根系中表达差异显著,且表达趋势相反的miRNAs包括miR167b、miR167g-5p、miR168a、miR171b。对其基因表达进行荧光实时定量(qRT-PCR)验证,并进一步对靶基因进行预测分析与功能研究,明确miR168a与其靶基因SlAGO1存在负调控关系并参与调控番茄的低钾胁迫响应。     

金星无核与其短节间突变体紫金早生的节间长度差异机制初探

【目的】探索金星无核短节间突变体紫金早生节间长度短缩的形成机制。【方法】以金星无核(JXWH)及其短节间突变体紫金早生(ZJZS)为研究材料,借助扫描电镜、LC-MS/MS和高通量测序分析两种材料在细胞形态、内源激素含量和miRNA上的差异。调查外源激素处理(JA及其合成抑制剂DIECA)下突变体节间长度的变化。【结果】紫金早生节间长度和节间细胞数量显著低于金星无核;紫金早生中JA、JA-ILE和SA含量显著提高,而ICA和ICAld含量显著降低;小RNA测序结果发现2种材料中共有21个差异miRNA,GO注释分析发现它们主要参与细胞分裂、茉莉酸代谢、蛋白代谢、环境应答和器官发育等过程。外源DIECA处理后,紫金早生节间伸长,外源JA处理抑制了紫金早生节间长度的伸长。【结论】紫金早生短节间突变性状与茉莉酸信号通路的调节有关,茉莉酸可能受miR319的调控。     

番茄LemiR390及其预测靶基因LeTAS3的鉴定与表达分析

以番茄（Lycopersicon esculentum）紫色花青素积累品系Aft基因型‘LA1996’为试验材料,以番茄总RNA反转录的cDNA文库为模板,根据mirbase数据库中MIR390基因和番茄unigene数据库预测到的靶基因序列,克隆番茄LemiR390前体基因及其预测靶基因LeTAS3;采用定量PCR技术检测LemiR390及其预测靶基因LeTAS3在番茄果实不同发育阶段的表达情况,利用RLM 5′RACE技术验证LemiR390对靶基因mRNA的剪切作用。结果表明,克隆到两个LemiR390的前体,分别与MIR390a和MIR390b一致,含有完整的茎环结构。LemiR390与其靶基因LeTAS3在番茄果实不同发育时期表达量不同,果实发育前期特别是花后1 ~ 2周幼果期表达量高,发育后期均下降为微量表达,并且在幼果期LemiR390与LeTAS3表达呈负调控关系。LemiR390能够靶作用于LeTAS3的转录本调控其降解,其剪切位点为LemiR390序列5′端的第10位碱基。     

基于microRNA深度测序的猕猴桃性别分化初探

利用新一代高通量测序技术,对猕猴桃雌花和雄花中表达的小RNA进行了测序,分别得到雌花18 408 610条序列和雄花11 191 469条序列。通过生物信息学分析,共鉴定和预测得到39个保守miRNA家族和400个新的miRNA家族,其中有170个miRNA家族在雌、雄花样品间显著差异表达。对差异表达miRNA进行靶基因的预测及注释,结果显示,靶基因产物具有包含核苷三磷酸水解酶的磷酸环结构域的miRNA数量最多。在猕猴桃25号连锁群（Chr25）上共预测得到3个miRNA,其中novel-ach-miR362的靶基因Achn298021可能与猕猴桃花的性别发育有关。     

库尔勒香梨9个新miRNA克隆鉴定

利用在小RNA高通量测序试验中筛选出的脱萼组与宿萼组差异表达新miRNA基因,采用 Stem-loop法对总体表达量居前20位、在脱萼组和宿萼组中具有显著性差异表达、在子房和萼片组织中具有显著性差异表达的新miRNA进行成熟体的克隆鉴定、前体序列二级结构分析、qRT-PCR试验以及靶基因预测。结果显示,在不同的样本中有9个新miRNA（novel_miRNA）的成熟体序列以及4个novel_miRNA的表达量与高通量测序结果完全一致,并且预测得到大量具有生物学功能的靶基因。新发现的miRNA可能与‘库尔勒香梨’萼片脱落和宿存有密切关系。     

基于高通量测序发掘番木瓜果实成熟相关miRNA

【目的】番木瓜是典型的呼吸跃变型果实,外源乙烯处理使番木瓜呼吸跃变提前,促进果实成熟。分离番木瓜果实成熟相关miRNA,为深入了解呼吸跃变型果实的成熟分子机制奠定基础。【方法】利用高通量测序技术对乙烯(ETH)、1-MCP和清水对照(CG)处理的番木瓜果实进行miRNA和转录组高通量测序,然后对测序获得数据进行生物信息学分析,进行miRNA鉴定和靶基因预测,并与转录组测序结果进行关联分析。【结果】乙烯、1-MCP和对照处理分别获得10 734 196、16 486 803和16 067 290条纯净序列,共鉴定出523个miRNA。其中,已知miRNA个数为1-MCP(303)、CG(214)和ETH(239),新miRNA个数为1-MCP(184)、CG(188)和ETH(114)。与对照相比,在乙烯处理中上调和下调表达的miRNA分别是123和72条。靶基因预测共获得5 053个靶基因,KEGG功能富集分析显示它们参与了戊糖、葡萄糖醛酸转换、淀粉和蔗糖代谢、卟啉和叶绿素代谢、类胡萝卜素合成等代谢途径。筛选出的番木瓜果实成熟衰老相关候选miRNA,包含4个果实软化调控相关miRNA(miR167-y、miR4993-x、miR3946-x和miR5059-x)、3个果实颜色调控相关miRNA(miR4993-x、miR815-y和miR7810-x)、3个激素调控相关miRNA(miR4993-x、miR8004-x和miR9722-x)和4个转录因子调控相关miRNA(miR5641-y、miR9722-x、miR838-y和miR319-y)。【结论】筛选的番木瓜果实成熟衰老相关miRNA为今后果实成熟衰老调控网络研究提供了可能的线索。     

番茄AP2/ERF超家族重鉴定及过表达SlERF.D.3株系表型分析

基于番茄基因组数据库的更新，系统地对番茄AP2/ERF超家族成员进行了更新，并对其进行了染色体定位、保守基序、基因结构和对灰霉菌及生长素胁迫响应的分析。共鉴定出141个ERF家族基因，其中新鉴定出的ERF亚家族成员42个；随机分布在12条染色体上，大都只含有外显子而无内含子，部分基因不同程度的受到灰霉菌和生长素处理的诱导表达。作为拟南芥AtERF109在番茄中的同源基因，SlERF.D.3的表达可被灰霉菌抑制且可迅速强烈地响应生长素处理。为进一步明确SlERF.D.3的生物学功能，以番茄‘Ailsa Craig’为材料克隆了此基因的编码区，构建过表达载体并转化番茄，获得了3个T0代过表达株系。与野生型相比，转基因株系的叶片较细长、向下卷曲，且果实出现乳状突起。这为研究SlERF.D.3在调节番茄的生长发育和胁迫响应过程中的作用奠定了基础。     

香蕉枯萎病菌Dicer-like基因的功能分析

香蕉枯萎病病原菌尖孢镰刀菌古巴专化型（Fusarium oxysporum f. sp. cubense）4号生理小种（Foc4）含有两个进化上高度保守的Dicer-like基因FocDCL1和FocDCL2。为了探究该基因的功能及其在RNAi中的作用机制，利用同源重组的方法获得ΔFocDCL1、ΔFocDCL2和ΔFocDCL1/2基因敲除突变体。表型分析显示，与Foc4野生型相比，突变体菌丝的营养生长无显著差异，但产孢量下降；ΔFocDCL2突变体在非生物胁迫刚果红处理后菌落明显变小且气生菌丝增多；ΔFocDCL2和ΔFocDCL1/2的致病力下降。miRNA深度测序数据显示，与Foc4野生型相比，ΔFocDCL1、ΔFocDCL2和ΔFocDCL1/2敲除突变体的miRNA长度分布和5′–端首位碱基出现频率都发生了改变，都能产生自身特异miRNA。DCL功能存在交叉和冗余，miRNA可以通过依赖独立的、交叉的或者联合的DCL发生；此外，鉴定到不依赖DCL形成的miRNA。这些结果表明FocDCL在产孢量、非生物胁迫、致病力以及小RNA发生中发挥作用。     

低夜温下番茄ABA缺失突变体和野生型叶片中miRNA差异表达分析

为揭示番茄叶片中miRNA对非生物胁迫的响应机制,以番茄ABA缺失突变体sit和野生型番茄RR为试验材料。采用实时荧光定量（qRT-PCR）技术检测叶片中6个miRNA（miR160、miR162、miR166、miR1919、miR397和miR6026）及其预测的靶基因在夜间低温和喷施外源ABA逆境胁迫下的表达情况。结果表明,在15 ℃夜温（对照）下,sit的ABA含量是60 ng · g^-1,RR是120 ng · g^-1,sit叶片的保卫细胞和气孔的开度都明显大于野生型RR,ABA缺失突变体sit中miRNA的表达量与野生型RR相比都显著下调,其靶基因除miR1919外,表达量都上调;夜间低温（6 ℃）处理12 h后,所有miRNA在sit中比RR中的表达量都显著增加;喷施80 mg · L^-1的ABA后,sit中miR162、miR166、miR1919及miR397比0 mg · L^-1 ABA处理的表达量显著上调。推测miR160、miR162和miR6026通过依赖ABA信号途径参与夜间低温胁迫。     

枣树阶段转变相关microRNA家族的鉴定及其表达分析

与其他果树相比,枣树具有童期短、成花快的特征.已有研究表明,多个microRNA(miRNA)家族参与植物阶段转变和开花时间调控等过程.研究枣树阶段转变相关的miRNA家族对果树童期调控具有重要意义.以枣实生后代植株不同发育阶段(节位)的当年生枝(枣吊)为材料,通过Small RNA测序,在童期、过渡期和成年期等3个时...     

miR-92b-5p attenuates renal injury and inflammatory response in diabetic nephropathy rats by targeting HMGB1

AIM To investigate the effect of microRNA-92b-5p （miR-92b-5p） on renal injury and inflammatory response in diabetic nephropathy （DN） rats and its mechanism. METHODS The rats were divided into control group， DN group， lentiviral negative control （LV-NC） group， LV-miR-92b group， LV-high mobility group protein B1 （LV-HMGB1） group and miR-92b+HMGB1 group， with 15 rats in each group. After fasting for 12 h， the model rats were intraperitoneally injected with streptozotocin at dose of 60 mg/kg， and the control rats were intraperitoneally injected with an equal volume of citrate buffer. Three days later， the rats in each treatment group were intravenously injected with 100 μL LV-NC， LV-miR-92b and LV-HMGB1 （1×10¹¹ U/L） twice a week for 8 consecutive weeks. Urinary protein， blood glucose， blood urea nitrogen and serum creatinine were detected by an automatic biochemical analyzer. The expression of miR-92b-5p and HMGB1 mRNA was detected by RT-qPCR. The targeting relationship between miR-92b-5p and HMGB1 was verified by dual-luciferase reporter assay. HMGB1 expression in kidney tissue was detected by Western blot. The kidney damage was observed by HE staining. The apoptosis was detected by flow cytometry. The levels of interleukin-6 （IL-6）， IL-1β and tumor necrosis factor-α （TNF-α） in renal tissues were detected by ELISA. RESULTS In DN model rats， miR-92b-5p was down-regulated， while HMGB1 was highly expressed. There was a binding site between miR-92b-5p and HMGB1 3'-untranslated region. High expression of miR-92b-5p inhibited the luciferase activity of the wild-type HMGB1 plasmid （P<0.01）， but had no effect on the luciferase activity of the mutant HMGB1 plasmid. Compared with DN group， urinary protein， blood glucose， serum creatinine and blood urea nitrogen in LV-miR-92b group were significantly reduced （P<0.01）. The degree of hyperplasia， swelling and inflammatory cell infiltration of glomerular mesangium and basement membrane tubules， the apoptosis rate of renal tissues， and the content of IL-6， IL-1β and TNF-α in renal tissues were significantly decreased （P<0.01）. Co-transfection of LV-HMGB1 significantly reversed the effect of miR-92b-5p on DN rats. CONCLUSION miR-92b-5p reduces renal injury and inflammatory response in DN rats by targeting HMGB1 and down-regulating its expression.     

Microarray-based miRNAs profiling in lower limb arteriosclerosis of diabetic rats

AIM: To establish the profiling of microRNAs (miRNAs) in the lower extremity arterial tissue between diabetic rats with lower limb arteriosclerosis (DAS) and diabetic rats with normal lower limb (DN), and to explore the possible molecular mechanisms involved in aberrant miRNA expression in DAS. METHODS: The rat models of DAS and DN were successfully established. The respective lower extremity arterial tissue was isolated. The total miRNAs were purified for a hybridization detection by miRNA microarray. The results of chip scanning and data were analyzed and verified by RT-qPCR. RESULTS: Ten miRNAs related to DAS, including rno-miR-206-3p, rno-miR-133a-5p, rno-miR-133b-3p, rno-miR-133a-3p, rno-miR-325-5p, rno-miR-675-3p, rno-miR-411-5p, rno-miR-329-3p, rno-miR-335 and rno-miR-126a-3p, were determined. All 10 abnormally expressed miRNAs were up-regulated. The validating results of RT-qPCR confirmed 9 of the miRNAs in line with chip expression. Just rno-miR-335 showed the opposite between PCR detection and microarray result. CONCLUSION: A group of miRNAs in diabetic rats suffering from lower limb arteriosclerosis plays an important role in the vascular atherosclerosis process. The abnormal expression of miRNAs is likely to affect the vascular atherosclerosis process.     

Expression of miRNA-198 and miRNA-296-5P in PB3A-treated colon cancer cell line and its function prediction

AIM:To explore the effect of pinobanksin-3-acetate (PB3A) on microRNA (miRNA) expression profile of human colon cancer cells for providing new methods of treatment of colon cancer and development of targeted drug.METHODS:The method of miRNA expression profiling was used to observe the miRNA differential expression in human colon cancer SW480 cells after treated with PB3A.The expression of miRNA-198 and miRNA-296-5p in the SW480 cells was detected by RT-qPCR.The network databases of miRWalk,MicroT,miRanda and so on were used to predict the target genes regulated by these miRNAs,and pathway significant enrichment analysis was performed.RESULTS:miRNA microarray analysis showed that after treated with propolis flavonoid PB3A for 24 h,267 miRNAs with differential expression twice or more in the SW480 cells were observed.Among them,there were 30 miRNAs with 10-fold or more differential expression,in which 28 were up-regulated and 2 were down-regulated.The results of RT-qPCR showed that the expression levels of miRNA-198 and miRNA-296-5p were consistent with the results of miRNA microarray analysis,and the difference was statistically significant (P<0.05).Bioinformatic analysis revealed that miRNA-198 has 859 target genes,and miRNA-296-5p has 906 target genes.The target genes of miRNA-198 were clustered in pathways in cancer,axon guidance,Wnt signaling pathway,regulation of actin cytoskeleton,insulin signaling pathway and MAPK signaling pathway,while the target genes of miRNA-296-5p were clustered in axon guidance,Wnt signaling pathway,MAPK signaling pathway,endocytosis,melanogenesis,insulin signaling pathway and calcium signaling pathway.CONCLUSION:Propolis flavonoid PB3A affects the expression of miRNA in colon cancer SW480 cells.The abnormal expression of miRNA-198 and miRNA-296-5p may be involved in the inhibitory effect of PB3A on colon cancer.     

Relationship between radioresistance and microRNA in the same genetic background nasopharyngeal carcinoma cells

AIM:To discuss the relationship between the discrepancy of microRNA (miRNA) and radioresistance in nasopharyngeal carcinoma (NPC) cells CNE-2R and CNE-2 on the basis of validating their different radioresistance.METHODS:Following the exposure of X ray on the clones of CNE-2R and CNE-2 cells, the dose-survival curve and biological characteristics of CNE-2R and CNE-2 cells were determined by SigmaPlot software and the linear quadratic model of survival curve analysis.MicroRNAs were detected by μParafloTM microfluidic chip, hybridization images collected by a laser scanner (GenePix 4000B, Molecular Device) and the signals normalized by a LOWESS filter.The relationship between the discrepancy of NPC radioresistance and the expression of miRNA was predicted according to Targetscan3.1 database (http://www.targetscan.org) after analyzing the data.RESULTS:Compared to CNE-2 cells, 37 miRNAs were gain-of-function and 29 miRNAs were loss-of- function in CNE-2R cells among 719 detected miRNAs.12 miRNAs that detective value was more than 2 000 and 2 folds than the other were hsa-miR-200b, hsa-miR-224, hsa-miR-26b, hsa-miR-125a-5p, hsa-miR-205, hsa-let-7e, hsa-let-7g, hsa-miR-19b, hsa-miR-24, hsa-miR-103, hsa-miR-106b and hsa-miR-93.Data showed that the distinct discrepancy of miRNAs was related to radioresistance.CONCLUSION:The discrepancy of miRNAs is present in different radioresistant NPC cell lines and related to radioresistance.     

Effects of miR-92a and miR-19b on insulin gene expression in mouse pancreatic β-cells

AIM To investigate the effect of microRNA-92a （miR-92a） and microRNA-19b （miR-19b） on the insulin expression in mouse pancreatic β-cells. METHODS The relative expression levels of endogenous miR-92a and miR-19b in mouse insulinoma MIN6 cells were detected by qPCR. The MIN6 cells were divided into control group， and experimental groups I and II， with 3 samples in each group， and transfected with negative control miRNA （NC）， miR-92a and miR-19b， respectively. The over-expression of the miRNAs was detected by qPCR. The morphological changes and viability of the cells were detected by optical microscopy and CCK8 assay， respectively. The expression of insulin was detected by qPCR， Western blot and immunofluorescence. The possible mechanisms of miR-92a and miR-19b regulating insulin expression were analyzed by bioinformatics prediction， dual-luciferase reporter assay， and Western blot. RESULTS Compared with the adult pancreatic progenitor cells， the expression of endogenous miR-92a and miR-19b in the MIN6 cells was decreased significantly （P<0.05）. Over-expression of miR-92a and miR-19b had no effect on the viability of MIN6 cells， but inhibited the expression of insulin at mRNA and protein levels. miR-19b significantly inhibited the luciferase activity of NeuroD1 3′UTR and the protein expression of NeuroD1 （P<0.05）. miR-92a had a fine-tuning effect on the luciferase activity of NeuroD1 3′UTR and the protein expression of NeuroD1. CONCLUSION miR-92a and miR-19b inhibit the insulin expression in mouse pancreatic β-cells.     

Functional analysis of differential microRNA expression profile in mouse fibrotic liver tissues induced by CCl4

AIM:To discover the expression profile of microRNAs (miRNAs) in mouse fibrotic liver tissues induced by carbon tetrachloride (CCl4), and to investigate the functions of these differential miRNAs based on the gene ontology (GO) analysis and KEGG Pathway analysis. METHODS:The mice were randomly divided into normal group and model group. Liver fibrosis was induced by subcutaneous injection of CCl4. miRNA expression profile of the liver tissues was assayed by a mouse miRNA microarray (Agilent 12.0). The differential expression of miRNAs between the normal and model mice was screened, and GO analysis and KEGG Pathway analysis were performed to determine the functions of these differential miRNAs. RESULTS:Thirty-nine miRNAs with differential expression were discovered in the model mice compared with the normal mice, among which 23 were up-regulated and 16 were down-regulated. GO analysis and KEGG Pathway analysis indicated that most pathological processes of liver fibrosis regulated by miRNAs included cell proliferation and activation, cell apoptosis, cell cycle, cell adhesion, inflammatory reaction, cell migration, transforming growth factor β (TGF-β) signaling pathway, Wnt signaling pathway and proteometabolism process. GO analysis revealed that the key up-regulated miRNAs were mmu-miR-322, mmu-miR-15b, mmu-miR-195, mmu-miR-200b and mmu-miR-214, and the key down-regulated miRNAs were mmu-miR-16, mmu-miR-130a, mmu-miR-101b, mmu-miR-30a and mmu-miR-30e. Analyzing the target genes screened out by GO analysis and Pathway analysis simultaneously, we found that the key up-regulated miRNAs included mmu-miR-200b, mmu-miR-322, mmu-miR-106b, mmu-miR-23a and mmu-miR-15b, and the key down-regulated miRNAs included mmu-miR-16, mmu-miR-30e, mmu-miR-30c, mmu-miR-30a and mmu-miR-130a. CONCLUSION: Differential expression of miRNAs is discovered in mouse fibrotic liver tissues induced by CCl4 compared with the normal liver tissues. Most of the pathological processes involved in liver fibrosis may be regulated by miRNA, such as cell proliferation and activation, cell adhesion and apoptosis, cell migration and differentiation, metabolism, TGF-β receptor signaling pathway and so on.     

Differential microRNA expression profile in laryngeal cancer and effect of miR-125a-5p on proliferation of laryngeal cancer cell line

AIM：To investigate the differential microRNA expression profiles between laryngeal cancer and adjacent normal laryngeal mucosa. METHODS：Forty two pairs of laryngeal cancer tissue and adjacent normal laryngeal mucosa tissue were collected. Ten pairs of samples were used for determining microRNA expression by the method of miRNA microarray chip. Data analysis was performed to find out the significant differential microRNA expression profile in laryngeal cancer, and the difference was verified by quantitative real-time PCR (qRT-PCR) analysis on another 32 pairs of samples. Methyl thiazolyl tetrazolium (MTT) assay and colony-forming assay were used to analyze the proliferation of Hep2 cells induced by miR-125a-5p. RESULTS：Both miRNA microarray and qRT-PCR showed that the expression of let-7f-5p, miR-10a-5p, miR-125a-5p, miR-144-3p, miR-195-5p and miR-203 was down-regulated in laryngeal cancer tissues. miR-125a-5p suppressed the proliferation of Hep2 cells. CONCLUSION：The results of microarray are accordant with those of qRT-PCR. Significant difference of miRNA expression profiles between laryngeal cancer and adjacent normal laryngeal mucosa indicates that miRNAs may play a role in carcinogenesis and progression of laryngeal cancer. miR-125a-5p inhibits the proliferation of Hep2 cell, indicating a novel therapeutic target against laryngeal cancer.