长链非编码RNA——病毒与宿主相互作用中的新型调控因子

长链非编码RNA（long non-coding RNAs，lncRNAs）是一类长度>200 nt的非编码RNA，在多种生物学过程中发挥重要调控作用。近年来研究表明，lncRNAs可被病毒诱导表达，其作为一类新型的调控因子介导宿主与病毒相互作用，通过病原识别受体，以不同机制激活或抑制天然免疫应答反馈病毒感染。本文阐述了lncRNAs介导病毒与宿主相互作用中的调控机制，归纳了它们在宿主抗病毒天然免疫应答过程中的调控网络，以期为研究lncRNAs在抗病毒中的作用提供参考，为揭示病毒的致病机制和发现新的抗病毒靶标奠定基础。     

长链非编码RNA是新的调控因子

近年来长链非编码RNA(Long non-coding RNAs,lncRNAs)在多个物种中的研究逐渐升温。lncRNAs属于非编码RNA类型,在各物种中普遍存在。研究发现,lncRNAs在发育过程中对重要相关基因具有调控作用。越是在发育复杂的高等生物体中,其基因组产生越多的lncRNAs,其与生物进化呈正相关。在本文中,综述了lncRNAs作为重要的调控因子参与胚胎发育、染色体失活、神经发育等过程,为进一步研究lncRNAs提供参考。     

调控动物性状相关长链非编码RNA的研究进展

长链非编码RNA(long non-coding RNA,lncRNA)是基因转录过程中产生的一类长度大于200个核苷酸(nt)的非编码RNA(non-coding RNA,ncRNA)。lncRNA的表达水平通常低于mRNA,且无高度保守序列,缺少开放阅读框,但它们具有更强的组织特异性表达模式。lncRNA可以通过与DNA、RNA(mRNA,miRNA,环状RNA)和蛋白质进行相互作用来发挥其功能,因此可作为信号分子、诱导物等来调节复杂的基因表达网络。作为一种新的调节分子,lncRNA正在成为基因表达调控中新的重要参与者,且近年研究表明,其与家畜动物性状调控密切相连。本文对lncRNA在动物肌肉生长分化、脂肪沉积、毛囊发育和繁殖方面进行了综述,旨在为lncRNA在家畜遗传育种上的应用提供依据。     

幼龄和成年太行山羊附睾头差异竞争性内源RNAs机制分析

旨在筛选出幼龄和成年太行山羊附睾头中差异表达的长链非编码RNAs(lncRNAs)、微小RNAs(miRNAs)和mRNAs,构建太行山羊附睾头中免疫相关基因调控的竞争性内源RNAs(ceRNAs)网络.本研究选取健康状况良好、体重相近的幼龄(2月龄)和成年太行山羊(2周岁)公羊各3只,去势采集其附睾头组织进行全转录组...     

脂肪相关lncRNAs在动物中的研究进展

脂肪是动物体内重要的储能物质，与动物的瘦肉率等重要的经济性状密切相关。脂肪发育是一个复杂而精密的过程，受到多种脂肪生成相关基因、转录调节因子及表观遗传因子的共同调控。长链非编码RNAs （long non-coding RNAs，lncRNAs）是一类长度>200 nt的非编码RNAs，可以在转录、转录后及表观修饰等多个水平上调节靶基因的表达，进而调控生命活动。近年来有关lncRNAs的研究逐渐增多，其作用范围几乎覆盖了生命活动的各个方面，也有一些lncRNAs被证实在脂肪发育的过程中发挥重要的调控作用，如棕色脂肪lncRNA 1（Blnc1）可以通过核糖核蛋白复合物促进棕色和米色脂肪细胞分化，该复合物也能够与早期B细胞因子2（Ebf2）起作用以增强产热基因如解偶联蛋白1（Ucp1）的表达；lnc-BATE1是棕色脂肪组织形成和结合异质核核糖核蛋白U （hnRNPU）以发挥产热作用所需的调控因子；lncRNA SRA能与过氧化物酶体增殖物激活受体γ（PPARγ）结合并增强PPARγ活性及其他多种途径，促进前脂肪细胞向脂肪细胞的分化，进一步调控脂肪的功能。作者对lncRNAs的基本特征、作用机制及其研究方法等，以及国内外对于脂肪发育相关lncRNAs的研究结果进行了综述，以期为进一步探索lncRNAs对脂肪发育的调控机制提供参考。     

影响藏猪与大约克夏猪肌肉品质的lncRNA的筛选及功能分析

旨在分析藏猪和大约克夏猪(180日龄)背最长肌组织中与猪肉质性状相关的长链非编码RNA (lncRNAs)和基因,探讨lncRNAs在猪肉品质中的分子调控作用,为猪肉质性状的改良提供理论依据.本研究根据先前公布的数据,以饲养在相同条件下的180日龄健康藏公猪(n-3)和大约克夏公猪(n-3)为研究对象,收集背最长肌肉品...     

Emerging Involvement of long non-coding RNAs in gastrointestinal associated inflammatory disorders

Gastrointestinal (GI) disorders including a wide range of infectious, inflammatory, autoimmune, etc. disorders. Inflammatory bowel and celiac disease are non-fatal but overwhelming GI associated disorders. IBD and celiac’s complications, besides the great suffering, disturb the normal life of the patients and make them involved in mental and physical problems. The emerging role of genetic content is deniable for GI inflammatory disorders incidence, and long non-coding RNAs (lncRNAs) function is the recent topic for its association. Analyzing of absolute lncRNAs interference in GI inflammatory appearance remains in infancy, and more studies are requested. Here, we concisely performed a systematic review in the last knowledge up to 2020 to identify all of the significant lncRNAs associated with the initiation and progression of GI inflammatory diseases. Accordingly, this assay attempted to refer to the expression of lncRNAs changing from the normal state, discovery of genetic mechanisms, and main effectors that would trigger associated IBD and celiac expression and immune responses would be effective for therapeutic approaches. It could be useful for prognostic and diagnostic purposes of GI associated inflammatory disorders.     

中国美利奴羊胚胎骨骼肌发育的加权基因共表达网络分析

旨在对绵羊胚胎骨骼肌lncRNAs（long non-coding RNA）进行鉴定分析,以阐明其在肌纤维类型转换与肌纤维增粗过程中的调控机制。本研究选取体重相近的成年中国美利奴母羊进行同期发情和人工授精,通过全转录组测序技术对其妊娠第85（D85N）、105（D105N）和135天（D135N）的胎儿背最长肌组织进行测序,设置D85N vs D105N、D105N vs D135N和D85N vs D135N 3个比较组,通过比较筛选出显著差异表达的lncRNA与mRNA。利用加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）方法构建共表达模块,使用DAVID在线工具和R-package进行GO和KEGG富集分析以找到与肌肉发育相关的模块。最后从目标模块中筛选出高连通度的lncRNAs和mRNAs,通过它们与miRNAs间的靶向预测关系建立lncRNA-miRNA-mRNA共表达网络。根据WGCNA分析结果,共得到25个模块。功能富集显示,模块中的核心基因主要富集于细胞粘附、Wnt、紧密连接、mTOR、AMPK及ECM-受体相互作用等肌肉发育相关的信号通路,选出模块中连通度高的lncRNAs和mRNAs构建子网络,得到TNNI2、PIP5K1A、PDK4等关键相关基因,预测出MSTRG.3903、MSTRG.10154、MSTRG.1629、MSTRG.10496、MSTRG.9559、MSTRG.10178、MSTRG.10521、MSTRG.3911、MSTRG.4586、MSTRG.7232等10个与肌肉发育、肌肉疾病、细胞增殖相关的lncRNAs。本研究成功构建了肌纤维发育相关的lncRNA-miRNA-mRNA共表达网络,找到多个与妊娠后期胚胎骨骼肌发育相关的潜在候选基因,为深入研究lncRNA在中国美利奴羊胚胎发育过程中骨骼肌的发育调控机制奠定了基础,也为其他家畜骨骼肌发育机制的研究提供了参考和方向。     

发情周期不同阶段绵羊卵巢lncRNA的鉴定和功能分析

旨在分析不同繁殖周期绵羊卵巢组织中长链非编码RNA (long non-coding RNA,lncRNA)的表达谱,了解lncRNA表达及其调控机理,为绵羊繁育研究提供理论依据。本研究以湖羊为研究对象,选取年龄在1.5～2.5岁的黄体期和卵泡期母羊各3只,通过高通量测序筛选出卵巢组织中的lncRNA,运用生物信息学分析对差异表达的lncRNA进行靶基因预测,通过GO和KEGG富集分析找出与绵羊繁殖相关的通路。结果显示,本研究共获得1 379个差异表达的lncRNAs,其中1 158个表达上调,221个表达下调。GO和KEGG富集分析表明,差异表达的lncRNAs及其靶基因主要参与卵泡发育、排卵周期过程、钙离子信号通路、卵母细胞减数分裂、催产素信号通路、MAPK信号通路、甲状腺激素合成通路、雌激素信号通路。关键的lncRNAs可能通过调控参与这些信号通路和生物学过程的相关基因来调控生殖。其中,LNC_011239、LNC_012847、LNC_003902、LNC_003906、LNC_003907等靶向的MAPK1、ADCY1、ADCY5、PPP3CA和CDC23可能发挥关键的调控作用。qRT-PCR验证证明,随机选取的5个差异lncRNAs定量结果与测序结果基本一致。本研究利用RNA-Seq技术筛选出黄体期和卵泡期卵巢组织中的lncRNAs,并进行差异分析,为揭示绵羊繁殖能力的分子机制提供依据。     

Long non‐coding RNA analysis of muscular responses to testosterone deficiency in Huainan male pigs

Long non‐coding RNAs (lncRNAs) participated in growth and development of skeletal muscle; however, little is known about their response to testosterone deficiency in porcine skeletal muscle. We compared lean mass related carcass traits and lncRNAs expression files in Longissimus dorsi (LD) muscle between intact and castrated Huainan male pigs. The results showed that castration significantly reduced eye muscle area and lean meat percentage (P < 0.05), but increased the fat mass weight (P < 0.05). Meanwhile, 8946 lncRNAs, including 6743 intergenic lncRNAs (lincRNAs), 498 anti‐sense lncRNAs, and 1705 intronic lncRNAs, were identified in porcine LD, among which, 385 lncRNAs were considered as the differentially expressed candidates between intact groups and castrated groups (q‐value < 0.05). Functional analysis indicated that these differently expressed lncRNAs and their target genes were involved in the estrogen receptor signaling pathway and skeletal and muscular system development and function. We first detect porcine muscular lncRNA response to castration, and the results suggested that lncRNAs and their target genes participated in the regulation of testosterone deficiency‐related skeletal muscle growth.     

五指山猪皮下脂肪组织lncRNA和mRNA的鉴定与分析

为了鉴定和分析五指山猪背部和腹部皮下脂肪组织中差异表达的长链非编码RNA(long noncoding RNA, lncRNA)和信使RNA(messenger RNA, mRNA),采用RNA-Seq和生物信息学方法对五指山猪皮下脂肪组织中的lncRNA和mRNA进行分析筛选,运用DESeq鉴定背部和腹部皮下脂肪组织中差异表达的lncRNA和mRNA,并对差异表达的lncRNA进行靶基因预测分析。结果显示:在五指山猪皮下脂肪组织中共鉴定出12 875个lncRNA,其中正义型10 155个、反义型278个、内含子型246个、基因间型2 196个;在背部与腹部皮下脂肪间,存在184个差异表达的mRNA,其中前十位分别是ZIC1、ZIC4、HAND2、CCBE1、RPH3A、ISM1、ANXA8、SLITRK4、DSG2、EVPL,存在45个差异表达的lncRNA,其中6个只在背部皮下脂肪中表达、18个只在腹部皮下脂肪中表达;获得差异表达lncRNA的靶基因共109个,包括顺式作用的靶基因和反式作用的靶基因。本试验为进一步研究lncRNA和mRNA调控猪皮下脂肪发育的分子机制提供科学依据。     

外泌体长链非编码RNA对脂代谢调控机制的研究进展

外泌体（exosomes）是一类由细胞分泌并且可远距离传递生物信息的纳米级胞外囊泡。它通过细胞分泌释放，在体液中传播，最后被其他细胞吞噬以达到传递生物信息的作用。脂类代谢一直是生命科学研究领域的热点，虽然影响脂质代谢的长链非编码RNA（lncRNA）很多，但外泌体中影响脂质代谢的lncRNA研究却相对较少。基于这个原因，对于外泌体源lncRNA的研究就十分必要。作为外泌体所携带的重要遗传物质之一，lncRNA是一类长度 > 200 nt的RNA分子，行使着诸如转录激活、染色质修饰等许多重要的生物功能。文章介绍了外泌体源lncRNA的生物学特点，列举了外泌体源lncRNA通过不同的分子机制来直接或间接的对脂质代谢产生影响的实例，分析了外泌体源lncRNA由于表达异常所导致的脂类代谢疾病，并且举例说明了外泌体源lncRNA作为生物标记的原理，最后对外泌体源lncRNA可作为家畜脂肪沉积生物标记功能的前景做了展望。如果在未来的研究中有更多的外泌体源lncRNA被检出，并足够对脂类代谢异常情况进行标记的话，那么对于预测和调控家畜脂肪沉积无疑会产生积极的意义。     

低温胁迫下民猪骨骼肌的转录调控分析

为了揭示民猪优良种质特性的遗传机理,解析其低温适应机制。本试验将6头6月龄体重相近的雌性民猪随机分成2组,每组3头个体。对照组个体置于温度控制在（18±2）℃的猪舍内,试验组个体置于室外的半敞篷舍内饲养,环境温度从第1天的5℃/-5℃降到最后1天的-15℃/-24℃,共处理了58 d。两组个体均保证自由采食和饮水,试验结束后,屠宰全部个体,取背最长肌进行RNA-seq。筛选民猪骨骼肌受低温诱导的基因和lncRNA,并对它们进行功能注释以及两者间调控关系的分析。RNA测序分析显示,民猪在经历58 d的低温胁迫后,骨骼肌内86个基因发生了显著上调,16个基因发生了显著下调;112个lncRNAs发生了显著上调,74个lncRNAs发生了显著下调。在发生显著上调的基因中,有4个与神经系统相关的基因NTSR2、ARC、FOSL1和RCAN1发生了显著上调,7个与基质转运相关的基因SLC2A4、SLC2A5、SLC4A10、SLC19A2、SLC20A1、SLC28A1和SLC38A2,6个与炎症和免疫相关的基因AREG、CISH、OTUD1、TRIB1、GPA33和ITPKC均发生了显著上调。而与昼夜节律相关的ARNTL基因和抑制细胞增殖的RASL11A基因等发生了显著下调。低温胁迫下,差异表达基因显著富集到细胞凋亡、直肠癌和癌症的转录误调节通路,说明细胞的增殖和凋亡受到影响。显著变化的lncRNA主要以反式调控作用于靶基因,且与靶基因间的互作关系复杂,它们调控的靶基因富集到单纯疱疹病毒1感染通路、MAPK信号通路和范可尼贫血通路。此外,再无其他通路受到影响。低温胁迫影响了民猪的神经和免疫系统,使细胞内的物质转运发生了变化,细胞的生长、分化也受到了影响,但由于基因发生变化的倍数较小（1～2倍为主）,且受影响的通路较少（仅3条）,因此推测低温胁迫并未对民猪的骨骼肌造成严重损伤。     

Identification of IGF2BP1-related lncRNA-miRNA-mRNA network in goat skeletal muscle satellite cells

Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in the proliferation of skeletal muscle satellite cells (MuSCs). Increasing evidence has shown that IGF2BP1 regulates the expression of noncoding RNAs and mRNAs. However, the related molecular network remains to be fully understood. Therefore, we performed RNA sequencing and analyzed the microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and mRNAs differentially expressed in goat MuSCs treated with IGF2BP1 overexpressing and empty vectors. A total of 36 miRNAs, 59 lncRNAs, and 44 mRNAs were differentially expressed caused by IGF2BP1. Expectedly, they were enriched in muscle development-related Rap1, PI3K-AKT, and FoxO signaling pathways. Finally, we constructed a lncRNA-miRNA-mRNA interaction network containing 30 lncRNAs, 15 miRNAs, and 34 mRNAs, in which several miRNAs, including miR-133a-3p, miR-204-5p, miR-125a-3p, miR-145-3p, and miR-423-5p, relate with cell growth and participate in muscle development. Overall, we constructed an IGF2BP1-related network, which provides new insight into the myogenic proliferation of goat.     

Influenza viruses and intracellular signalling pathways

It has been described in the last years that after influenza virus-infection a variety of intracellular signalling pathways have been induced. There are examples and suggestions how the viral replication cycle leads to the activation of intracellular signalling pathways. A variety of signalling pathways are activated after virus-infection as an alert-response against the invading pathogen that can be considered as an antiviral response of the host cell. Nevertheless, it was also shown, that viruses are able to suppress these cellular responses to assure their own replication. Moreover, viruses are also able to activate and misuse cellular signalling pathways for their own survival. The NF-kappaB signalling pathway is an excellent example of these sceneries. Activation of the NF-kappaB signalling pathway mediated by the virus can partially be blocked by the NS1 protein to suppress a strong antiviral IFN alpha/beta response. At the same time the virus takes advantage of the remaining NF-kappaB activity for virus related apoptosis and for its own replication. This is a highly effective and economic way for the virus to control its replication without the need for specific viral inducers of cellular responses. This demonstrates, that there are no "all or nothing" reactions in the field of interactions of Influenza viruses with intracellular signalling pathways. In one situation cellular antiviral responses can be misused by the virus of its own replication and at another point the same signalling pathway may even be turned into a pro-viral activity. When the impact of a given signalling pathway on viral growth is evaluated these bivalent functions of these pathways should be taken in consideration. Nevertheless, a signalling pathway that supports viral growth is an excellent target for antiviral therapy (Ludwig et al. 2003).     

非洲猪瘟病毒感染后猪外周血淋巴细胞Toll样受体信号通路的lncRNA-mRNA分析

【目的】丰富非洲猪瘟病毒（African swine fever virus,ASFV）感染后猪外周血淋巴细胞长链非编码RNA（long non-coding RNA,lncRNA）表达谱,并进一步挖掘影响Toll样受体信号通路的调控网络。【方法】试验动物感染ASFV,于第7天采集外周血并分离得到外周血淋巴细胞,运用Illumina高通量组学测序对外周血淋巴细胞中lncRNA进行测序,原始数据经处理后筛选获得差异表达的lncRNA,并进行靶基因预测,利用生物信息学方法对靶基因进行GO功能和KEGG信号通路富集分析,初步绘制与Toll样受体信号通路相关的lncRNA-mRNA调控网络,并对lncRNA-ENSSSCG00000041959在内的4个lncRNAs进行实时荧光定量RT-PCR验证。【结果】共筛选到73个差异表达的lncRNAs,其中上调表达lncRNAs 38个,下调表达lncRNAs 35个。GO功能分析结果显示,靶基因显著富集在调节免疫系统过程、防御反应、生物刺激、病毒反应和先天性免疫;KEGG信号通路富集分析显示,大部分靶基因与细胞循环、疾病及免疫应答有关,其中免疫相关信号通路有Toll样受体信号通路、TNF信号通路、产生IgA的肠道免疫网络等。进一步挖掘出lncRNA-ENSSSCG00000041959-RIPK1和lncRNA-ENSSSCG00000041959-IRAK1可能是影响Toll样受体信号通路的重要调控网络,实时荧光定量RT-PCR与测序结果一致。【结论】本研究初步鉴定出lncRNA-ENSSSCG00000041959-RIPK1和lncRNA-ENSSSCG00000041959-IRAK1可能是影响Toll样受体信号通路的lncRNA-mRNA调控网络,为进一步探索lncRNA调控ASFV感染机体免疫反应奠定了理论基础。