刺参响应灿烂弧菌侵染差异microRNAs鉴定及靶基因分析

microRNA参与基因的转录后调控,在真核生物的生长发育、细胞分化和免疫防御等过程中发挥重要作用。刺参(Apostichopus japonicus)病害问题已成为产业发展的主要限制因素之一,而其病害发生的分子机制尚待进一步完善。本研究以刺参重大疾病“腐皮综合征”的重要致病原灿烂弧菌(Vibrios splendidus)为侵染菌株,通过人工侵染实验制备患病刺参样本,采用miRNA-seq技术对侵染组(PT16S)和对照组(PT10H)各3头刺参的体壁组织进行miRNA测序,通过相关生物信息学软件对miRNAs进行鉴定和分析,筛选差异表达miRNAs (DEmiRNAs)并预测其靶基因,构建关键调控途径的miRNA-mRNA调控网络。结果显示,PT10H组平均得到5 902 588条有效序列,194个已知miRNA和19个新的miRNA;PT16S组平均得到5 053 529条有效序列,182个已知miRNA和42个新的miRNA。对2组鉴定到的miRNA进行差异表达分析,共筛选到2个上调和11个下调的具有显著差异的DEmiRNAs (P≤0.05),上调的DEmiRNAs靶基因预测结合到3010个靶基因,注释到585个GO terms及24条信号通路(P≤0.05),下调的DEmiRNAs靶基因预测到19 072个靶基因,注释到514个GO terms以及22条信号通路(P≤0.05)。对筛选到的DEmiRNAs进行实时荧光定量PCR (qRT-PCR)验证,显示miRNA-seq与qRT-PCR的一致率达到70%。根据KEGG分析结果构建泛素介导的蛋白水解途径和Notch信号通路的miRNA-mRNA调控网络,结果显示,13个DEmiRNAs分别靶向结合134个与泛素介导的蛋白水解相关的mRNAs和109个与Notch信号通路相关的mRNAs,Aja-miR-184、Aja-miR-2478和Aja-miR-9277p等DEmiRNAs可能参与对Notch信号通路和对泛素介导的蛋白水解的调控。相关研究结果将为刺参疾病发生调控网络建立和机制解析提供依据。     

硬骨鱼免疫相关microRNA研究进展

MicroRNA (miRNA)是一类长度为18～25 nt的非编码RNA,在硬骨鱼免疫应答中起重要作用。近年来,借助高通量测序与荧光定量PCR (RT-PCR)技术,筛选到大量免疫相关的差异表达miRNA (DE miRNA)。通过比较多种硬骨鱼在不同病毒/细菌感染条件的miRNA表达谱,筛选出相同DE miRNA,并认为筛选出的DE miRNA是潜在参与调节宿主免疫应答的进化上保守的候选DE miRNA。据此,我们在病毒感染表达谱中筛选到10个进化保守的DE miRNA,细菌感染表达谱中筛选到8个保守的DE miRNA。此外,miRNA的功能研究也取得较大进展,宿主miRNA不仅可直接抑制病毒的复制,同时参与调控干扰素反应、炎症、细胞凋亡等过程。本文简述了硬骨鱼免疫相关miRNA的研究进展,以期为硬骨鱼疾病预防与治疗提供新思路。     

拟穴青蟹miR-34靶基因预测及其生物信息学分析

MiR-34是一类在进化过程中高度保守的miRNA家族,参与机体的许多重要生命活动。本研究首先比较本实验室构建的拟穴青蟹miRNA数据库中的miR-34(spa-miR-34)和通过miRBase获得的多个物种的miR-34的序列特征,然后应用RNAhybrid和Segal Lab两种在线工具预测spa-miR-34的靶基因,用blast2go软件对这些靶基因进行功能注释和信号通路富集分析。结果表明,spa-miR-34可能的靶基因有66个,这些基因的功能主要包括氧化还原、磷酸化、钙离子跨膜运输、转录等生物学过程;信号通路主要富集于精氨酸和脯氨酸代谢、抗生素生物合成、苯丙素生物合成、糖酵解和糖异生等合成代谢通路中。spa-miR-34预测的靶基因所涉及的基因家族和通路亦包括CHH家族、ERK通路、细胞周期和UPP通路、SUMO通路。此外,spa-miR-34预测的靶基因还有蜕皮激素受体,推测spa-miR-34在生殖、蜕皮及氨基酸等物质代谢方面具有重要作用。本研究为进一步了解spa-miR-34在拟穴青蟹中的作用提供了重要参考资料。     

花鲈cox6a基因与相关miRNA的鉴定及其在盐度适应中的表达调控分析

细胞色素c氧化酶（COX）是线粒体电子传递链的末端酶,COX6A是细胞色素c氧化酶的核编码亚基之一。为丰富花鲈（基因及相关miRNAs在花鲈渗透调节机制中的潜在作用,本研究开展了花鲈cox6a基因的miRNAs,并对其与）。系统进化树分析进一步确认了两个花鲈在垂体、脑、肝脏和肾脏中的表达量较高,基因的miRNA：miR-30e-5p、miR-223、miR-200a-3p和miR-155-5p,但没有发现可能靶定基因以及miR-30e-5p、miR-223、miR-200a-3p都呈现显著差异表达,而miR-155-5p仅在适应高盐环境时出现了显著的差异表达。这表明,基因和4个miRNAs在花鲈的渗透调节过程中发挥潜在作用。其中miR-30e-5p、miR-223和miR-200a-3p的表达趋势与cox6a2基因的表达调控。本研究为探讨花鲈适应不同盐度环境的渗透调节机制提供了基础数据。     

快速高效miRNA分析流程在黄颡鱼中的应用

高通量测序技术速度快、成本低、通量高,广泛应用于miRNA领域研究。本研究基于高通量测序技术所产生的海量小RNA数据,结合已有的数据分析软件,开发了一套快速高效一键化的miRNA分析流程。该流程整合多个生物信息学数据分析软件,对多个miRNA高通量测序数据集进行标记、整合和去冗余分析,只需运行一次核心程序就可以实现对多个miRNA高通量测序数据的分析,避免每个样本单独数据分析的技术重复,精简后的数据集能大幅度减少软件计算量,显著提高软件运行效率。本研究利用快速高效miRNA分析流程分析黄颡鱼性腺XX卵巢、XY精巢、YY精巢的miRNA高通量测序数据,获得一批准确的黄颡鱼保守miRNA。在相同参数设置下,miRNA分析流程可以显著节约分析时间。该流程最终输出结果为多样本整合后的miRNA表达数据,便于研究者直接进行样本之间的比较和miRNA的表达差异,减少研究者手动整合分析结果的操作步骤。miRNA分析流程针对多样本miRNA测序数据具有明显的优势,样本越多测序量越大,软件运行效率越高。针对日益积累的海量小RNA测序数据,miRNA分析流程高效快速一键化数据处理优势将会越来越明显。     

长牡蛎性腺中调控型非编码RNA的生物信息学

本研究以日照海域同一家系的2龄长牡蛎性腺为研究对象,通过small RNA-seq和RNA-seq技术筛选和鉴定出大量的非编码微小RNA(mi RNA)、长链非编码RNA(lnc RNA)和环状RNA(circRNA),并对其进行了生物学特征分析。结果显示,以斑马鱼为参考序列,获得25～30个已知miRNA成熟体和51～63个已知miRNA前体,预测到53～71个新miRNA成熟体和53～77个新miRNA前体;长牡蛎miRNA长度分布为18～26个核苷酸(nt),其中分布在20～22 nt长度的miRNA数量最多,且miRNA首位碱基多为U。测序分析获得2 302～2 349个注释lncRNA转录本,预测到20 083～24 114个新lncRNA转录本,其中基因间型lncRNA(lincRNA)、内含子lncRNA(intronic lncRNA)、反义lncRNA(anti-sense lncRNA)分别占29.0%、62.1%和8.9%;长牡蛎lncRNA的基因组特征与其他真核生物的lncRNA基因组特征相似,与mRNA相比,外显子(exon)个数少,转录本长度较短,表达水平低。测序分析共获得383个circRNA,其中平均88.54%来源于exon,平均4.51%来源于intronic,平均6.95%来源于intergenic,且鉴定出内源性circRNA潜在大量的miRNA结合位点。研究结果为后续研究长牡蛎调控型ncRNA的表达规律和生物学功能奠定了基础。     

低氧胁迫下鲢miR-17a-5p及其靶基因分析

为了探究miR-17a-5p在鲢低氧胁迫下的功能,在前期鲢small RNA测序的基础上对鲢miR-17a-5p进行靶基因预测及功能富集分析,通过双荧光素酶活性验证其与HIF-1α的靶向关系,并检测低氧胁迫下miR-17a-5p和其靶基因在鲢肝脏、脑、心脏和鳃四个组织中的动态表达特征。结果显示,鲢miR-17a-5p在不同物种间高度保守,预测出381个miR-17a-5p的潜在靶基因显著富集在硫代谢、mTOR信号通路以及萜类骨架的生物合成3个KEGG信号通路上。miR-17a-5p可与HIF-1α mRNA的3′UTR结合,并降低HIF-1α mRNA水平,低氧胁迫下miR-17a-5p的表达呈下降趋势,而HIF-1α表达则呈上升趋势;3个显著富集KEGG通路中的11个miR-17a-5p潜在靶基因在低氧胁迫过程中的不同组织中的表达,尤其是肝脏中的表达,除SGK1外,均呈显著上升趋势。研究表明,低氧胁迫下鲢各组织中miR-17a-5p的表达下调减弱了其对靶基因的抑制作用,进而导致HIF-1α、ddit4和Lrp5等响应低氧胁迫的基因表达上调。本研究为低氧胁迫下鲢miRNA的表达与调控机...     

枯草芽孢杆菌对氨氮应答的转录组及sRNA分析

为探索枯草芽孢杆菌(Bacillus subtilis)脱氮的分子机制,筛选枯草芽孢杆菌对氨氮的分子生态学应答相关候选基因及small RNA(sRNA),本研究对处于富含氨氮环境和对照组的枯草芽孢杆菌R47进行原核链特异性转录组及sRNA分析,并采用Real-timePCR方法检测差异表达基因的相对表达量。结果显示,平均每个测序样本得到约1.40×10⁷条reads。对照组与处理组DESeq2分析得到3918个差异表达基因,并富集在KEGG数据库中的176个信号通路,其中,包括8个与适应富含氨氮环境相关的信号通路(细菌双组分系统通路、精氨酸生物合成、嘌呤代谢等),同时发现,epsA、tasA、sinR、glnR、glnA、tnrA和ureABC基因可能参与枯草芽孢杆菌对氨氮的应答过程。经sRNA分析获得已注释的枯草芽孢杆菌sRNA 62条。对sRNA靶基因的分析结果显示,其有3960个对应的潜在靶基因,主要参与碳水化合物运输和新陈代谢、氨基酸转运和代谢、转录过程,其中,sRNA2073和sRNA2182对应的靶基因分别为sinR和tnrA。Real-time PCR结果显示,argH、codY、argG、glnA和glnR基因的相对表达量变化与转录组测序结果一致。本研究为进一步探究枯草芽孢杆菌污水脱氮的分子机理提供参考数据。     

越冬期体色变异红罗非鱼差异表达miRNA的鉴定

为了探究红罗非鱼越冬期体色变异的分子机制，实验构建了其2种体色(正常粉红体色和变黑体色)皮肤组织的小RNA文库，每组4个重复，组装后平均每组分别获得12 190 544和11 891 890条过滤后的读长(clean reads)，获得miRNA成熟序列669个，其中337个是已知的miRNAs。鉴定出越冬期变黑体色相对于正常粉红体色鱼的差异表达miRNAs 26个，其中上调11个，下调15个，且12个为已知的miRNAs，可能在红罗非鱼越冬期体色变异过程中发挥重要作用。富集分析发现了大量代谢和体色调控相关的通路。研究表明，红罗非鱼越冬期的体色变异可能是色素细胞的增殖和迁移形成的，与代谢相关的调控通路在其中发挥重要作用，为解析红罗非鱼越冬期体色变异的机制奠定了基础。     

microRNA在水产动物中的研究进展

mi RNAs是一类在真核生物中广泛存在的非编码小分子RNA,通过与靶m RNA互补配对在转录水平上对基因的表达进行负调控,导致m RNA的翻译抑制或降解。大量研究表明,mi RNA在躯体发育、癌症、细胞分化、细胞增殖与凋亡、脂肪代谢等方面发挥作用。近来在水产动物中,有关mi RNA的研究取得了众多的科研成果,然而对其进行全面总结的报道较缺乏。本文综述了mi RNA在水产动物中的研究进展,结果显示mi RNA在水产动物中表现为多样化的生物学功能,本文也对其研究前景进行了展望,旨在为以后更好地研究水产动物mi RNA的功能提供参考。     

Differential expression of lipid metabolism‐related genes and miRNAs in Ctenopharyngodon idella liver in relation to fatty liver induced by high non‐protein energy diets

To explore the mechanism of fatty liver formation induced by high non‐protein energy diets in grass carp (Ctenopharyngodon idella), basal diet and high‐energy diets were fed to juvenile grass carp for 9 weeks. The experimental groups fed on high‐energy diets which included a high‐lipid diet (H‐LIP), a high‐carbohydrate diet (H‐CHO) and a high‐lipid and carbohydrate diet (H‐CL). The control group fed on basal diet. Growth performance, liver fat accumulation, serum biochemical indexes and the expression levels of lipid metabolism‐related genes (SREBP‐1, PPARγ, FAS, ACC1, and LPL) and miRNAs (miR‐33, miR‐122, and miR‐370) were examined at the end of the feeding trial. There were no significant differences in growth rate and feed efficiency among the four groups. However, significant increase in mesenteric and liver fat contents, and lipid droplets in the liver was induced by high‐lipid and high‐carbohydrate diets. There were significant differences in serum biochemical indicators such as AST/ALT, GLB, TG and TP, and liver fatty acid composition between the control and experimental groups. The expression levels of SREBP‐1, PPARγ, FAS, ACC1 and LPL were upregulated, while CPT‐1 was downregulated with the high‐energy treatments. Additionally, the expression levels of miR‐33, miR‐122 and miR‐370 in the liver were higher in the three high‐energy treatments than those in the control (P < 0.05). The results suggest that modifications of lipid metabolism‐related genes and miRNAs may be involved in fatty liver formation induced by high non‐protein energy diets in grass carp.     

Effects of sodium butyrate stimulation on immune‐related mRNA‐miRNA network in intestine of grass carp

Sodium butyrate is one of the most popular feed additives in animal husbandry. In recent years, sodium butyrate has been increasingly used as supplement in aquaculture. The present study is to investigate the intestinal mRNA and microRNA response to diet with sodium butyrate in grass carp (Ctenopharyngodon idella), an important aquaculture species in China. mRNA and microRNA profiles of intestine of grass carp fed with diet contained 0, 1.0, 2.5, 5.0, 7.5 and 10.0 g/kg sodium butyrate were obtained by RNA‐seq using Illumina Hiseq 2,500 platform. The feeding trial was performed using 18 individuals of 1‐year‐old grass carp (n = 3 for each group) and lasted for 40 days in tanks in laboratory. A total of 349,860,852 sequence reads were generated from six intestinal libraries. Functional analysis of differentially expressed genes showed that genes participated in immune pathways tend to be activated by sodium butyrate supplementation. A total of 700 microRNAs were obtained, including 275 conserved microRNAs and 425 novel microRNAs which are potentially involved in regulating 14,300 genes. Spearman's correlation analysis identified 18 pairs of microRNA‐mRNA associated with immune pathways (p < .01 and R<?0.5). The potential genes targeted by microRNAs include CXCL12, AKT1S1, Cab39 and MHCII which are important genes associated with intestinal immune pathways. To our knowledge, this is the first integrated profiling of both mRNA and microRNA in intestine with supplementation of sodium butyrate in grass carp. The present results suggest that sodium butyrate affects intestinal immune system by regulating microRNA‐mRNA interaction in fish.     

Fructose 1,6 bisphosphatase activity in liver and gonads of sea bass (Dicentrarchus labrax). Influence of diet composition and stage of the reproductive cycle

The fructose 1,6 biphosphatase (FBPase) activity was measured in the liver and gonads of broodstock sea bass that were fed three experimental diets over the reproductive cycle. Enzyme activity was measured at the pre-spawning (November), spawning (February) and post-spawning (May) periods. Additionally, some biometric indices were calculated at these three times. The different diets, one with standard composition (51% protein, 13% lipid, 10% digestible carbohydrates), one with a high-carbohydrate content (32% protein, 13% lipid, 32% digestible carbohydrates) and one deficient in ω3 essential fatty acids (51% protein, 13% lipid, 10% digestible carbohydrates), had similar affects on growth and gonad development, as deduced from the similar weight, condition factor, hepatosomatic index, gonadosomatic index and liposomatic index over the reproductive cycle. FBPase activity was detected at all times in the liver of both sexes, and in the ovaries but not in the testes. In general, females showed greater liver activity than males, especially at spawning time. During post-spawning, FBPase activity fell in tissues of both sexes. Enzyme activity was also affected, mostly in the liver, by the different types of feed; hepatic activity in fish fed the high-carbohydrate diet fell during the spawning and post-spawning periods, though at a different level for each sex. The diet deficient in ω3 EFA presented the lowest FBPase activity, compared with the other diets, in females during the spawning period; there was very little change in males or females over the reproductive cycle. The results showed that the highest gluconeogenic activity in sea bass broodstock occurred at the spawning time and the females had larger glucose requirements than males over the reproductive cycle, as demonstrated by the absence of FBPase activity in testes. This work also confirmed the adaptative capacity of this enzyme to different nutritional and physiological conditions.     

Effect of dietary zinc supplementation and phytase pre-treatment of soybean meal or corn gluten meal on growth, zinc status and zinc-related metabolism in rainbow trout, Oncorhynchus mykiss

Rainbow trout, Oncorhynchus mykiss, were fed diets containing untreated or phytase-treated soybean meal and corn gluten meal with or without 50 mg supplemental zinc kg–1 to determine if dietary phytate caused a zinc (Zn) deficiency. Fish fed diets containing untreated soybean meal and corn gluten meal without supplemental Zn (basal diet) showed no signs of a Zn deficiency after 170 d of weight gain. Weight gain, carcass protein content, total bone Zn, and alkaline phosphatase and carboxypeptidase B activities were not significantly altered in fish fed the basal diet. Dietary phytate removal and supplemental dietary Zn were not required to prevent Zn deficiency in rainbow trout fed a plant-based diet. Although bone Zn concentrations were reduced in fish fed the basal diet, total bone Zn increased in all fish regardless of dietary treatment. Future assessments of Zn status of fish should be based on changes in Zn-dependent metabolism or total bone Zn rather than on bone Zn concentration.     

褐牙鲆中miRNAs与甲状腺激素受体TRβ的相互作用研究

甲状腺激素通过与其受体结合对褐牙鲆变态起重要的调控作用,而miRNAs通过结合靶基因3′-UTR在转录后水平调节靶基因的表达。为探讨miRNAs在褐牙鲆变态中的作用,通过生物信息学方法预测褐牙鲆TRβ基因3′-UTR存在的miRNAs结合位点,并利用3′-RACE方法克隆TRβ基因的3′-UTR序列,通过体外DNA重组技术构建应用于miRNAs靶向基因检测的双荧光素酶重组报告载体,利用细胞转染和双荧光素酶报告技术分析多个miRNAs与TRβ基因的作用关系。研究结果显示,克隆得到了一段长为437 bp的褐牙鲆TRβ基因的3′-UTR序列,发现3′-UTR序列上存在pol-miR-125a、pol-miR-214、pol-miR-460-5p、pol-miR-138和pol-miR-125a*的结合位点,成功构建了双荧光素酶重组报告载体,命名为pmirGLO-TRβ-3′-UTR。双荧光素酶报告分析结果表明,pol-miR-125a、pol-miR-214、pol-miR-460-5p和pol-miR-138均为作用于褐牙鲆TRβ的靶向miRNAs,而pol-miR-125a*对TRβ基因无直接的调节作用。研究结果将为后续深入研究miRNAs与TRβ在褐牙鲆变态发育中的功能及其作用机制提供基础。     

Growth,feed utilization and metabolic responses of three gibel carp (Carassius gibelio) strains to fishmeal and plant protein‐based diets

The utilization of plant‐based diets in fishes could be affected by their genetic backgrounds. To examine this, three strains of one‐year‐old gibel carp, Dongting (strain DT: 30.42 ± 0.05 g), CAS III (strain A: 43.34 ± 0.08 g) and CAS Ⅴ (strain F: 61.78 ± 0.10 g), were fed fishmeal (FM), soybean meal (SBM) and rapeseed meal (RM) diets for 8 weeks. The present results showed that growth performances, feed utilization, body composition, postprandial kinetics of plasma metabolites and gene expression of lipid metabolism markers in the three strains were affected by diets and strains (p < 0.05). Strain A had higher SGR than strain DT and F (A > F > DT) with the three diets, whereas strain F had higher FE than the other two strains with FM and RM diets (p < 0.05). Compared to FM diet, plant protein‐based diets resulted in poor growth, feed use and nutrient retention in all the three strains, and different strains showed differing changes in fatty acid synthesis and oxidation to different dietary proteins. Overall, strain A showed better growth performances than the other two strains irrespective of diet, and all the three strains could utilize RM diet better than SBM diet.     

Optimal dietary taurine level for growth of juvenile Japanese flounder Paralichthys olivaceus

The requirement for taurine in juvenile Japanese flounder Paralichthys olivaceus was determined by feeding diets containing various levels of taurine and cystine. Test diets supplemented with 0.5, 1.0 and 1.5% of taurine or with 0.5, 1.0 and 1.5% of L -cystine were prepared. The basal diet contained 55% protein from white fish meal. These diets were fed to juvenile Japanese flounder with an initial mean bodyweight of 0.9 g (total length (TL) 48 mm) for 5 weeks. Approximately 1.4% taurine content in the diet was required for optimum growth of juvenile flounder. A positive linear relationship was noted between the content of taurine accumulated in the muscle, liver and brain and the level of taurine in the diet. However, there was no increased taurine content in tissues of fish fed the cystine-supplemented diet. In contrast, the fish fed control and cystine-supplemented diets showed higher contents of cystathionine in the tissues. The concentration of cystathionine in tissues rapidly decreased with an increase of taurine in the diet. It was also observed that for each of the dietary groups, a trace amount of taurine was excreted. These results suggest that the taurine content in the diet affects the sulfur amino acid metabolism of juvenile Japanese flounder, and indicate that juvenile flounder are unable to biosynthesize taurine from cystine.