可变剪接的理论工作研究进展

pre-mRNA的可变剪接是调控真核生物基因表达以及蛋白质多样性的重要机制,使得可变剪接与组织分化或疾病发生有密切联系。从序列水平和表达水平对可变剪接的理论工作研究进展做了介绍,主要由相关数据库和常见的生物信息学方法两部分组成。     

大白菜BrSPS1Fb基因剪接受体位点变异及其对剪接的影响

为研究剪接受体位点变异对剪接方式与效率的影响,对大白菜材料He2进行重测序,发现BrSPS1Fb-He2第6个内含子(I6)的剪接受体位点由AG突变为AC。对大白菜材料He2花瓣进行转录组测序并分析BrSPS1Fb-He2 read数据,结果显示,BrSPS1Fb-He2在pre-mRNA加工过程中发生了选择性剪接。BrSPS1Fb-He2可选择3个位置(A1、A2和A3)作为受体进行剪接,产生3种剪接异构体(S1、S2和S3),或者保留I6整个内含子,形成S4剪接异构体。大白菜BrSPS1Fb-He2的成熟mRNA中保留部分I6(S1和S2)或全部I6(S4),或者缺失部分E7外显子序列(S3)。综上,BrSPS1Fb剪接受体位点的单核苷酸多态性(single nucleotide polymorphisms,SNP)变异对其转录后剪接产生了显著影响。     

人类1号染色体可变剪接与普通剪接基因同义密码子的使用分析I.同义密码子偏爱使用分析

人类1号染色体可变剪接(选择性剪接)基因344非冗余蛋白质编码序列(188183密码子)和普通剪接(非可变剪接)基因的386蛋白质编码序列(223116密码子)被用于研究人类密码子使用偏爱模式.全部密码子使用数据分析表明,人类可变剪接基因密码子的偏爱水平显著高于普通剪接基因.在人类1号染色体基因中,密码子第三位置的G C含量有很大的异质性(0.24～0.95),并且可变剪接基因密码子第三位置平均G C含量(64.66%)大于普通剪接基因(59.97%).Nc值对GC3s图显示密码子偏爱使用除了受核苷酸组成制约外,其它的因子可能也影响密码子的使用变化.此外,可变剪接基因中以G 或C结尾的密码子比普通剪接基因出现的频率高.密码子使用的差异可能是由可变剪接基因pre-mRNA特有的结构特征和多种剪接模式决定的.     

TMV载体上发生的的前体mRNA基因剪接效应

根据以往的报道,TMV基因只存在于细胞质中且不发生基因剪接,前体mRNA(Pre-mR鄄NA)的剪接只能发生在细胞核中。本研究应用RT-PCR,DNA序列测定及GUS INTRON的点突变和荧光检测等研究手段,首次发现TMV载体中GUS基因的表达和前体mRNA的剪接同时发生,证明了GUS基因在TMV载体上的剪接效应。     

前沿动态

MOS11:mRNA出核运输中的一个新元件在真核细胞中,基因表达从转录和新生mRNA前体(pre-mRNA)的核内加工过程开始的,是一个多步骤的过程。mRNA出核是基因表达通路中的重要步骤和关键环节,直接影响真核细胞的生长、增殖、分化、发育等多种生命活动。许多重要疾病的发生与发展都与mRNA出核异常     

秀丽线虫缺氧相关剪接调节因子的筛查

【目的】基于RNA干涉文库,寻找与秀丽线虫缺氧损伤表型相关的剪接调节因子。【方法】利用喂饲RNA干涉(RNA interference,RNAi)文库筛选技术,对秀丽线虫基因组中的351个RNA结合蛋白(RNA bindingprotein,RBP)基因进行筛选。【结果】经过2次筛选共得到5个与缺氧相关的RBP编码基因,其中剪接因子1个,参与mRNA翻译过程的基因4个。【结论】剪接调节因子可能在mRNA的剪接和翻译水平上参与低氧应答。     

丙型肝炎病毒NS4B蛋白调控Hep3B细胞非折叠蛋白质反应研究

研究表达的丙型肝炎病毒(HCV)NS4B对Hep3B细胞非折叠蛋白质反应的影响。NS4B重组真核表达质粒pcDNA3.1(-)NS4B通过脂质体转染Hep3B细胞,G418筛选和Western blot鉴定稳定转染细胞;RT-PCR检测稳定转染细胞内XBP1 mRNA剪接,Western blot鉴定ATF6蛋白切割,荧光素酶试验检测稳定转染细胞内GRP78和XBP1启动子活性。G418筛选和Western Blot鉴定证实获得稳定表达NS4B的Hep3B细胞;在该细胞内,XBP1 mRNA剪接、ATF6切割、XBP1和Grp78启动子激活均被检测到。NS4B在Hep3B的稳定表达诱导了非折叠蛋白质反应。     

崂山奶山羊不同泌乳期乳腺组织可变剪接的鉴定与分析

本研究对崂山奶山羊泌乳初期、高峰期和末期乳腺组织RNA-Seq数据进行可变剪接分析,共鉴定到151 503个可变剪接事件,对应17 627个可变剪接基因,6 323个差异剪接基因,显著富集到细胞器、蛋白质结合、mRNA加工和RNA剪接等相关GO条目,主要参与催产素信号通路、钙信号通路、内质网中的蛋白质加工等,与乳腺组织生理活性密切相关的KEGG通路,筛选出PTEN作为参与乳腺发育及泌乳相关生理过程中调控网络的核心基因。研究结果表明,可变剪接在奶山羊不同泌乳期的乳腺组织具有发育阶段特异性,特有可变剪接基因与乳腺组织生理活性特点密切相关,在调控奶山羊乳腺组织发育及泌乳生理中发挥重要作用。本研究可为探究可变剪接机制调控奶山羊乳腺发育与泌乳性状的分子机理提供理论依据。     

豚鼠发情周期不同时期的子宫LHR mRNA差异表达研究

 【目的】克隆豚鼠子宫黄体生成素受体(LHR)基因片段并分析其进化关系,研究豚鼠子宫LHR mRNA在发情周期不同时期的表达特性。【方法】以豚鼠子宫总RNA为模板,根据小鼠、大鼠、猪LHR保守区设计引物,RT-PCR扩增LHR基因片段。筛选阳性克隆测序,采用DNAMAN软件分析比对同源性。以?-actin为分子内参,采用优化的半定量RT-PCR技术,测定豚鼠发情周期不同时期的子宫组织LHR mRNA表达量。【结果】测序得到686 bp的剪接变异体1和缺失75 bp 4号外显子的剪接变异体2。686 bp序列与人类LHR mRNA序列同源性为83.8%,与牛、猪及绵羊LHR mRNA序列同源性分别为84.6%、84.2%及83.6%,而与大鼠和小鼠LHR mRNA序列同源性则分别高达93.7%和99.4%。LHR mRNA在豚鼠整个发情周期的子宫中都有表达,发情周期第0天的表达水平为0.635 ± 0.0194,第4天为0.617 ± 0.099,均显著低于第8天的表达水平(P＜0.05),随之在第12天升至1.218 ± 0.049。【结论】克隆的片段为豚鼠LHR基因的部分序列,其mRNA存在着剪接变异体。豚鼠子宫LHR mRNA在发情周期第0、4天表达水平较低,第12天升至最高,即发情周期不同时期的LHR mRNA表达呈现明显的规律性,该结果为探究哺乳动物非性腺组织中LHR的功能及生殖内分泌调控机制提供了理论依据。     

转录因子bZIP60调控植物抗病抗逆的研究进展

未折叠蛋白反应(UPR)在植物的逆境胁迫、病原物侵染、生长发育中发挥重要作用,转录因子bZIP60是UPR信号之一。在明确了拟南芥、水稻、玉米、小麦等内质网应激时需肌醇酶(IRE1)介导bZIP60 mRNA剪接激活的基础上,归纳了bZIP60对逆境和病原物的响应机制,总结了IRE1/bZIP60信号在植物抗病抗逆中的研究进展。正常生长条件下,以前体蛋白bZIP60U的形式跨内质网膜。发生应激时,IRE1识别并剪切bZIP60 mRNA的双茎环结构,产生含转录激活域和核定位信号的活性蛋白bZIP60S,并在细胞核内形成二聚体,结合到应激反应相关基因的启动子,通过上调胁迫应答相关基因提高植株抗性。     

Affinity chromatography of splicing complexes: U2, U5, and U4 + U6 small nuclear ribonucleoprotein particles in the spliceosome

The splicing process, which removes intervening sequences from messenger RNA (mRNA) precursors is essential to gene expression in eukaryotic cells. This site-specific process requires precise sequence recognition at the boundaries of an intervening sequence, but the mechanism of this recognition is not understood. The splicing of mRNA precursors occurs in a multicomponent complex termed the spliceosome. Such an assembly of components is likely to play a key role in specifying those sequences to be spliced. In order to analyze spliceosome structure, a stringent approach was developed to obtain splicing complexes free of cellular contaminants. This approach is a form of affinity chromatography based on the high specificity of the biotin-streptavidin interaction. A minimum of three subunits: U2, U5, and U4 + U6 small nuclear ribonucleoprotein particles were identified in the 35S spliceosome structure, which also contains the bipartite RNA intermediate of splicing. A 25S presplicing complex contained only the U2 particle. The multiple subunit structure of the spliceosome has implications for the regulation of a splicing event and for its possible catalysis by ribozyme or ribozymes.     

牛ME1基因cDNA编码序列的克隆与分析

在NCBI中GenBank里查询已登录的牛的ME1 mRNA序列(GenBank Accession:XM-613987),发现其1-69 bp序列与已知的人、猪和小鼠的ME1基因mRNA序列没有任何相似性,因此,认为这段序列有误。研究利用人的ME1基因mRNA序列作为电子探针共找到44段牛的相关ESTs序列,然后利用此ESTs重叠群拼接成的序列设计了三对引物。提取牛的肝脏和肌肉总RNA,从中克隆测序得到M1为525 bp、M2为1039 bp和M3为1171bp的三段序列,拼接成长度为2015 bp的序列。此段序列与前述ESTs重叠群一致序列完全相同,并与人、猪和小鼠的ME1基因mRNA序列相似性分别达89%、85%和84%,从而证实了本序列的正确性。本序列已在NCBI登录(GenBank Accession:FJ495084)。研究为进一步研究牛的ME1基因结构提供了真实的序列信息。     

烟草PR3b转录后剪切元件NRSE1与GUS融合表达后的可变剪切

【目的】烟草（Nicotiana tabacum L.）碱性几丁质酶基因PR3b在低烟碱突变体（nic1和nic2）中存在转录后mRNA可变剪切现象,但其可变剪切的发生机制仍不清楚。将PR3b的可变剪切元件NRSE1（nicotine- synthesis related splicing element 1）与GUS融合表达,分析NRSE1元件的独立可变剪切特性,以揭示其作用机制。【方法】利用PCR扩增方法获得PR3b cDNA序列中的NRSE1元件片段,并利用基因重组技术构建了烟草PR3b可变剪切元件NRSE1与GUS的融合表达载体。将融合表达载体导入农杆菌LBA4404后,通过农杆菌介导的叶盘转化法培育了表达NRSE1与GUS融合子的低烟碱突变体nic1和nic2及野生型烟草转基因植株;通过RT-PCR检测及GUS染色鉴定出阳性植株后,利用RT-PCR分析NRSE1与GUS融合表达后在低烟碱突变体和野生型烟草中的可变剪切特性;对转基因植株的幼苗进行乙烯（ET）和茉莉酸（JA）处理,通过GUS染色方法分析ET和JA处理对转基因植株中GUS活性的影响,并通过RT-PCR方法分析ET和JA处理对转基因植株中NRSE1与GUS融合子的可变剪切特性影响,以及对转基因植株中NRSE1与GUS融合子表达水平的影响。【结果】通过RT-PCR检测及GUS染色鉴定出表达NRSE1元件与GUS融合子的低烟碱突变体和野生型烟草转基因植株;RT-PCR检测及测序分析证明,NRSE1元件与GUS融合表达后仍能在低烟碱突变体发生高水平的可变剪切,剪切修饰区段的序列变化与烟草中PR3b的mRNA可变剪切修饰一致;利用ET和JA处理转基因植株进行的GUS染色表明,ET和JA处理对转基因植株的GUS活性有不同程度的影响;但利用ET和JA处理转基因植株进行的RT-PCR分析表明,ET和JA处理不改变NRSE1元件原有的诱导剪切特性,也不影响转基因植株中NRSE1元件与GUS融合子的表达水平。【结论】PR3b的可变剪切元件NRSE1与GUS在烟草中融合表达后,仍能在低烟碱突变体nic1和nic2中发生高水平的可变剪切;NRSE1在烟草中的可变剪切不依赖PR3b的其他mRNA区段,是烟草PR3b发生可变剪切的独立元件;ET和JA处理对NRSE1元件与GUS融合表达植株的GUS活性具有一定影响,可能存在翻译水平的调控作用。     

Predictive identification of exonic splicing enhancers in human genes

Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing. A computational method, RESCUE-ESE, was developed that predicts which sequences have ESE activity by statistical analysis of exon-intron and splice site composition. When large data sets of human gene sequences were used, this method identified 10 predicted ESE motifs. Representatives of all 10 motifs were found to display enhancer activity in vivo, whereas point mutants of these sequences exhibited sharply reduced activity. The motifs identified enable prediction of the splicing phenotypes of exonic mutations in human genes.     

山羊SDHD基因cDNA编码序列的克隆与分析

利用NCBI中GenBank里查询到已登录的人、猪、牛和绵羊的SDHD mRNA序列,通过多重同源比较,从而获得高度保守区域序列,设计了同源引物,并首次对山羊SDHD编码序列进行了分子克隆。经过PCR扩增和测序,获得山羊SDHD基因共4段cDNA序列,分别为:451 bp4、20 bp5、29 bp和698 bp。所获得的四段序列测序结果经La-sergene7.0软件SeqMan拼接后,获得一条1238 bp长的cDNA序列。在GenBank数据库中进行BLAST/nr比对,发现其与绵羊、牛、猪和人相应序列相似性分别达98%、97%、85%和81%。用NCBI的ORF Finder软件对已经克隆的山羊SDHD基因cDNA进行开放阅读框分析,发现该序列包含一个480 bp的开放阅读框,编码159个氨基酸残基,计算机分析表明(Compute pI/Mw tool),该蛋白的分子量约为17 224.11 Da,等电点为8.92。通过DNAMAN软件分析发现,山羊SDHD蛋白保守性很高,其与绵羊、牛、猪和人SDHD蛋白在氨基酸序列上的相似性分别达到97%、96%、87%和85%。此山羊SDHD基因cDNA序列和SDHD蛋白质序列已于2010年1月31日登录在NCBI的GenBank上,登录号为GU338978和ADB92501。本项研究为进一步研究山羊的SDHD基因作为山羊肉品质性状候选基因,提供了相应的序列信息。     

Regulated splicing of the Drosophila P transposable element third intron in vitro: somatic repression

In eukaryotic cells alternative splicing of messenger RNA precursors (pre-mRNA's) is a means of regulating gene expression. Although a number of the components that participate in regulating some alternative splicing events have been identified by molecular genetic procedures, the elucidation of the biochemical mechanisms governing alternative splicing requires in vitro reaction systems. The tissue specificity of P element transposition in Drosophila depends on the germline restriction of pre-mRNA splicing of the P element third intron (IVS3). Drosophila P element IVS3 pre-mRNA substrates were spliced accurately in vitro in heterologous human cell extracts but not in Drosophila somatic cell splicing extracts. Components in Drosophila somatic cell extracts that specifically inhibited IVS3 splicing in vitro were detected by a complementation assay. Biochemical assays for Drosophila RNA binding proteins were then used to detect a 97-kilodalton protein that interacts specifically with 5' exon sequences previously implicated in the control of IVS3 splicing in vivo. Inhibition of IVS3 splicing in vitro could be correlated with binding of the 97-kD protein to 5' exon sequences, suggesting that one aspect of IVS3 tissue-specific splicing involves somatic repression by specific RNA-protein interactions.     

Nuclear factors in B lymphoma enhance splicing of mouse membrane-bound mu mRNA in Xenopus oocytes

Regulation of the synthesis of membrane-bound and secreted immunoglobulin mu heavy chains at the level of RNA processing is an important element for B cell development. The precursor mu RNA is either polyadenylated at the upstream poly(A) site (for the secreted form) or spliced (for the membrane-bound form) in a mutually exclusive manner. When the mouse mu gene linked to the SV40/HSV-TK hybrid promoter was microinjected into Xenopus oocytes, the mu messenger RNA (mRNA) was altered by coinjection of nuclei of mouse surface IgM-bearing B-lymphoma cells to include the synthesis of the membrane-bound form. An increase in the membrane-bound form was not observed when nuclei of IgM-secreting hybridoma cells or fibroblast cells were coinjected. Deletion of the upstream poly(A) site did not eliminate the effect of B-lymphoma nuclei suggesting that membrane-specific splicing is stimulated. Further, splicing of other mu gene introns was not affected by coinjection of B-lymphoma nuclei. These results suggest that mature B cells contain one or more transacting nuclear factors that stimulate splicing specific for membrane-bound mu mRNA.     

Expression of the pX gene of HTLV-I: general splicing mechanism in the HTLV family

Human T-cell leukemia virus type I (HTLV-I) is an etiological agent of adult T-cell leukemia. A viral gene pX encodes for p40X and it has been proposed that this protein trans-activates the viral long terminal repeat and possibly some cellular genes; this activation may be associated with T-cell transformation. The mechanism of pX gene expression and the primary structure of p40X are now reported. Two-step splicing generates the 2.1-kilobase pX mRNA; the initiator methionine for env becomes part of the pX protein. These splicing signals are conserved among all members of the HTLV family except for the acquired immune deficiency syndrome-associated viruses.