木薯可溶性淀粉合成酶(MeSSⅡb)启动子克隆及梯度缺失分析

木薯淀粉被广泛用作各种食品、饲料及工业淀粉制品的原材料。然而目前,国内外还未见木薯可溶性淀粉合成酶基因Me SSs的启动子相关研究报道。本研究通过在木薯基因组数据库中查询Me SSⅡb基因第一个外显子及其上游序列,通过PCR扩增获得Me SSⅡb上游序列。对获得的上游序列通过Plant CARE及PLACE进行启动子结构及元件分析,并与其它物种中SSSs基因启动子区序列利用BLAST进行比对分析后,确立翻译起始位点上游1 566 bp序列为启动子区,进而设计并构建了包括完整启动子在内的5'端梯度缺失启动子融合GUS蛋白植物表达载体p E1566::GUS、p E1356::GUS、p E1116::GUS、p E531::GUS、p E453::GUS、p E387::GUS、p E138::GUS转化本氏烟草进行启动子活性验证。利用叶盘侵染法转化本氏烟草进行启动子梯度缺失分析后发现,缺失启动子p E1356、p E1116、p E531活性丧失,缺失至翻译起始位点上游138 bp的缺失启动子p E138,仍具有启动子活性。上述表明,在克隆启动子区1 566 bp片段中,在-1 566 bp和-1 356 bp之间210 bp序列片段对于完整启动子活性尤为重要,而-1 356 bp至-531 bp之间存在启动抑制因子,在-453 bp和-138 bp为基础启动序列,初步推断为转录起始结合位点。     

人及小鼠钠通道SCN3A基因的启动子及其上游调控区的分析

为了比较研究人与小鼠SCN3A基因的启动子及其上游调控区的特征,采用5′-Full RAGE方法对人及小鼠SCN3A基因的转录起始点进行了准确定位,通过序列测定及对比分析证明:确定人和小鼠SCN3A基因的转录起始点均为"A",人SCN3A基因转录起始点位于翻译起始点上游约27 kb处,而小鼠位于翻译起始点上游约31 kb处.人SCN3A基因5′非翻译区存在两个5′非翻译外显子,而小鼠只有一个5′非翻译外显子.人和小鼠SCN3A基因核心启动子区(-80～+70)的同源率高达96.0%,存在相同的启动子核心元件,BRE/和TATA;在-400至+200区段内预测到人存在而小鼠不存在的转录因子有PHR1、GATA-1、FOXN2、NF-及AP-4,小鼠存在而人不存在的转录因子Sp、Sp3及GBF.人和小鼠SCN3A启动子区特征的异同将为进一步研究该基因在人和小鼠的表达调控机制提供重要线索.     

水稻种子醇溶蛋白4a基因的表达受串联复合启动子调控

从水稻中花8号中克隆了醇溶蛋白4a的基因5＇侧翼区并首次报道该基因5＇端-680～-18区段具有胚乳特异性表达调控功能.本研究通过 5’缺失方法对该基因5＇侧翼区的结构和功能进行了进一步分析,结果表明:(1)醇溶蛋白4a基因启动子Ⅰ能够特定地在转基因烟草开花发育 22 d后的种子胚乳中激活下游 GUS融合基因表达,是该基因有功能的启动子;(2)prolamin box Ⅱ对该基因的表达具有增强功能;(3)启动子Ⅰ的转录起始点是位于该基因起始ATG上游63 bp处的C碱基.     

DMD/BMD缺失基因的检测及其表达产物的变化

目的:检测Duchenne/Becker型肌营养不良症(DMD/BMD)患者基因缺失及其表达产物--抗肌营养不良蛋白在肌细胞中的变化,探讨其与临床病情的关系.方法:应用9对引物多重PCR技术对42例DMD/BMD患者进行基因检测;并采用免疫荧光抗体染色技术对5例DMD,2例BMD肌细胞膜上抗肌营养不良蛋白的表达观察分析,以2例正常人的肌组织作为对照.结果:共发现21例外显子缺失,缺失片段长度各异,其中16例(76.2%)累及中央缺失热区,5例(23.8%)位于5'端缺失热区,尤以48号外显子缺失频率最高.5例DMD患者胞膜抗肌营养不良蛋白染色阴性,其中1例未检出基因缺失,但抗肌营养不良蛋白无表达.2例BMD患者染色弱阳性,可见间断斑片状荧光带.结论:DMD/BMD病情轻重可能与基因缺失的数量和片段大小不呈平行关系,而是与外显子的缺失类型有密切关系;基因的表达受个体差异的影响,呈高度的遗传异质性.抗肌营养不良蛋白缺乏或表达异常是造成DMD/BMD表型的病理基础,其临床后果不仅取决于缺失程度,还取决于缺失区域的功能意义.     

依赖PrfA转录调控的单核细胞增生李斯特菌毒力基因inlC启动子结构特点的初步研究

为了研究单核细胞增生李斯特菌毒力基因启动子的结构特点与转录调控因子PrfA蛋白之间的关系,应用PCR定点突变和重组PCR技术缺失了该菌毒力基因inlC启动子上可能与PrfA蛋白结合以及诱发转录起始相关的碱基序列,构建了一系列突变启动子与lacZ报告基因融合表达质粒,使lacZ基因的表达置于inlC突变启动子下,并分别电转化单核细胞增生李斯特菌野生株P14、PrfA蛋白高表达突变株P14a和prfA基因等位缺失突变株A42中,检测相应的β-半乳糖苷酶活性。结果表明:位于inlC启动子转录起始点下游22bp处的一段17bp的类似PrfA蛋白结合序列TTAACAGCGTTTGTTAA并没有增强和抑制PrfA转录调控活性的功能;甚至将其改造成“完美的”PrfA蛋白结合序列TTAACATTTGTTAA后,也不影响inlC依赖于PrfA的转录活性地表达;但是,如果缺失inlC启动子上原始的PrfA蛋白结合序列,则使inlC依赖于PrfA的转录活性完全丧失;另外,单核细胞增生李斯特菌毒力基因inlC和plcA依赖于PrfA的转录活性的表达也与启动子上PrfA蛋白结合区(PrfA-box)距离-10区的碱基个数有关:最适为22或23bp,长于23bp或短于22bp的突变启动子的依赖PrfA的转录活性大大降低,甚至没有活性。说明除PrfA蛋白结合序列外,受PrfA调控的毒力基因启动子上还可能存在其它尚未阐明的结构和序列影响PrfA蛋白的结合以及启动转录表达。     

中国汉族个体HLA-A、-B基因全长序列的测定及调控区多态性

文章利用20个中国汉族个体样本建立了稳定精确的HLA-A、-B基因全长序列的克隆测序方法, 获得HLA-A 10个等位基因4.2 kb序列, HLA-B 6个等位基因3.7 kb序列, 序列涵盖了两个基因的所有外显子、所有内含子、5′启动子区以及3′非翻译区(3′UTR)。A*1153是文章发现的一个新等位基因, B*151101的内含子序列、5个HLA-A以及2个HLA-B等位基因的5′启动子序列和3′UTR序列为国际上首次报道, 其他等位基因均延伸了IMGT/HLA数据库中释放的全长序列。文章首次在中国汉族个体中测定了IMGT/HLA数据库中没有覆盖的HLA-A、-B基因的上游5′启动子以及下游3′UTR区域的多态性模式。HLA-A基因5′启动子延伸区域共发现26个SNPs和一处3 bp(AAA/-)的插入/缺失, 3′UTR延伸区域共发现14个SNPs; HLA-B基因5′启动子延伸区域共发现5个SNPs和一处1 bp(T/-)的插入/缺失, 3′UTR延伸区域共发现8个SNPs。通过对两个基因的5′启动子、外显子以及3′UTR的系统发育树分析, 发现两个基因调控区与外显子的进化关系有所不同, HLA-A基因除A*24020101外, 其他等位基因两端调控区与外显子连锁比较紧密, HLA-B基因两端调控区与外显子之间则发生了较为频繁的重组事件。     

依赖PrfA转录调控的单核细胞增生李斯特菌毒力基因inlC启动子结构特点的初步研究

为了研究单核细胞增生李斯特菌毒力基因启动子的结构特点与转录调控因子PrfA蛋白之间的关系,应用PCR定点突变和重组PCR技术缺失了该菌毒力基因inlC启动子上可能与PrfA蛋白结合以及诱发转录起始相关的碱基序列,构建了一系列突变启动子与lacZ报告基因融合表达质粒, 使lacZ基因的表达置于inlC突变启动子下,并分别电转化单核细胞增生李斯特菌野生株P14、PrfA蛋白高表达突变株P14a 和prfA基因等位缺失突变株A42中,检测相应的β-半乳糖苷酶活性。结果表明：位于inlC启动子转录起始点下游22bp 处的一段17bp的类似PrfA蛋白结合序列TTAACAGCGTTTGTTAA并没有增强和抑制PrfA转录调控活性的功能;甚至将其改造成“完美的” PrfA蛋白结合序列TTAACATTTGTTAA后,也不影响inlC依赖于PrfA的转录活性地表达;但是,如果缺失inlC启动子上原始的PrfA蛋白结合序列,则使inlC依赖于PrfA的转录活性完全丧失;另外,单核细胞增生李斯特菌毒力基因inlC和plcA 依赖于PrfA的转录活性的表达也与启动子上PrfA蛋白结合区(PrfA-box)距离-10区的碱基个数有关:最适为22或23bp,长于23bp或短于22bp的突变启动子的依赖PrfA的转录活性大大降低,甚至没有活性。说明除PrfA蛋白结合序列外,受PrfA调控的毒力基因启动子上还可能存在其它尚未阐明的结构和序列影响PrfA蛋白的结合以及启动转录表达。     

大肠杆菌精氨酰tRNA合成酶基因（argS）的上游非编码区存在一个负调控区

含大肠杆菌精氨酰tRNA合成酶（ArgRS）基因(argS）的pUC18重组质粒,在大肠杆菌TG1转化子中能够高表达ArgRS近1000倍。为了研究大肠杆菌argS的表达调控,构建了一系列的缺失突变。分别缺失全部上游序列（argS△1）、Shine-Dalgarno（SD）区（argS△2）和缺失启动子－10区下游（相当于翻译起始位点－65nt,argS△3）前的上游序列后的变种argS都不能表达ArgRS。而缺失－122nt（距翻译起始位点－180nt,argS△8）、－70nt（距翻译起始位点－128nt,argS△7）、－52nt（距翻译起始位点－110nt,argS△6）、－35区9距翻译起始位点－94nt,argS△5）、启动子－10区（距翻译起始位点－71nt,argS△4）前的上游序列后,这些缺失突变基因的表达水平与野生型argS接近。但argS△4、argS△5、argS△6都会形成部分包涵体。通过RNA斑点杂交测定发现,argS△4、argS△5和argS△6的mRNA转录量为argS及argS△7的2到3倍。即－52nt和－70nt之间的19个碱基（AATAGTGAAAACGGCAATA)可能是大肠杆菌argS舞场康负调控区。该元件的缺失将使得ArgRS过快表达并导致部分蛋白质形成包涵体。凝胶阻滞分析也发现在细胞粗抽液中有一个因子可以专一地与这个负调控元件结合,它可能参与该基因的表达调控。精氨酸专一性地诱导argS的转录,其作用与上述转录负调控区相关。     

水稻OsNRT1-d启动子的分离和功能分析

采用PCR技术,从水稻基因组中分离到OsNRT1-d读码框上游2 019 bp序列.序列分析表明:在起始密码ATG上游-189 bp和-127 bp处分别存在CAAT-box和TATA-box,具有典型的启动子结构.推测的转录起始位点CAC位于起始密码ATG上游-93 bp处.将OsNRT1-d启动子5′-端系列缺失后,分别与GUS报告基因融合,获得的NRT2019∷GUS、NRT1196∷GUS 和NRT719∷GUS转基因载体.农杆菌介导转化水稻,获得的转基因水稻均能启动下游GUS报告基因在水稻的根、叶、花颖和种子中表达;将转基因水稻幼苗放在滤纸上紧急干旱处理和用15% PEG6000进行模拟干旱处理,GUS基因的表达量明显升高,且干旱应答元件在-719 bp～-1 bp的范围内;GUS活性分析表明:OsNRT1-d启动子对ABA、NaCl、(NH4)2SO4、KNO3和Gln等信号没有应答反应.     

应用PCR技术对DMD患者进行缺失检测与产前基因诊断

运用聚合酶链式反应(polymerasechainreaction,PCR)技术对3个Duchenne型肌营养不良症(DMD)家系中的患者进行dystrophin基因内9个外显子缺失检测,在2个家系中检测到外显子45、48、51缺失,同时运用PCR技术扩增位于dystrophin基因内内含子短串联重复序列,对非缺失型DMD家系进行了产前诊断,胎儿为正常女性.dystrophin基因外显子缺失检测方法快速、敏感、准确,可在临床推广中应用;短串联重复序列(STR)多态性分析方法可用于DMD家系的产前基因诊断和携带者检出.     

Frameshift deletions of exons 3-7 and revertant fibers in Duchenne muscular dystrophy: mechanisms of dystrophin production.

Duchenne muscular dystrophy (DMD) patients with mutations that disrupt the translational reading frame produce little or no dystrophin. Two exceptions are the deletion of exons 3-7 and the occurrence of rare dystrophin-positive fibers (revertant fibers) in muscle of DMD patients. Antibodies directed against the amino-terminus and the 5' end of exon 8 did not detect dystrophin in muscle from patients who have a deletion of exons 3-7. However, in all cases, dystrophin was detected with an antibody directed against the 3' end of exon 8. The most likely method of dystrophin production in these cases is initiation at a new start codon in exon 8. We also studied two patients who have revertant fibers: one had an inherited duplication of exons 5-7, which, on immunostaining, showed two types of revertant fibers; and the second patient had a 2-bp nonsense mutation in exon 51, which creates a cryptic splice site. An in-frame mRNA that uses this splice site in exon 51 was detected. Immunostaining demonstrated the presence of the 3' end of exon 51, which is in agreement with the use of this mRNA in revertant fibers. The most likely method of dystrophin production in these fibers is a second mutation that restores the reading frame.     

Antisense PMO Found in Dystrophic Dog Model Was Effective in Cells from Exon 7-Deleted DMD Patient

Background

Antisense oligonucleotide-induced exon skipping is a promising approach for treatment of Duchenne muscular dystrophy (DMD). We have systemically administered an antisense phosphorodiamidate morpholino oligomer (PMO) targeting dystrophin exons 6 and 8 to a dog with canine X-linked muscular dystrophy in Japan (CXMD_J) lacking exon 7 and achieved recovery of dystrophin in skeletal muscle. To date, however, antisense chemical compounds used in DMD animal models have not been directly applied to a DMD patient having the same type of exon deletion. We recently identified a DMD patient with an exon 7 deletion and tried direct translation of the antisense PMO used in dog models to the DMD patient''s cells.

Methodology/Principal Findings

We converted fibroblasts of CXMD_J and the DMD patient to myotubes by FACS-aided MyoD transduction. Antisense PMOs targeting identical regions of dog and human dystrophin exons 6 and 8 were designed. These antisense PMOs were mixed and administered as a cocktail to either dog or human cells in vitro. In the CXMD_J and human DMD cells, we observed a similar efficacy of skipping of exons 6 and 8 and a similar extent of dystrophin protein recovery. The accompanying skipping of exon 9, which did not alter the reading frame, was different between cells of these two species.

Conclusion/Significance

Antisense PMOs, the effectiveness of which has been demonstrated in a dog model, achieved multi-exon skipping of dystrophin gene on the FACS-aided MyoD-transduced fibroblasts from an exon 7-deleted DMD patient, suggesting the feasibility of systemic multi-exon skipping in humans.     

Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy.

The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random "libraries" of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25-60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1-41, and we now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes.     

Detection of gene deletions in Chinese patients with Duchenne/Becker muscular dystrophy using CDNA probes and the polymerase chain reaction method.

One hundred thirty-eight patients with Duchenne/Becker muscular dystrophy (DMD/BMD) were screened with complete cDNA probes and the multiplex polymerase chain reaction (mPCR) amplification of 18 pairs of oligonucleotide primers. Eighty-six deletions and 4 duplications were detected, the deletion frequency being 62.3%. Eighty-two deletions were detected with the two sets of primers described by Chamberlain et al. and Beggs et al, which was 95.4% of deletions detected by complete cDNA probes. Consistent with the deletion locations described previously, the deletions of dystrophin gene in Chinese individuals are clustered mainly in two high-frequency deletion regions of exons 44-52 (68.6%) of 3' side of the gene central regions and exons 1-19 (26.7%) in the 5' side. The distribution of deletions in dystrophin gene is associated with the phenotype of DMD/BMD. In the 25 cases with in-frame deletions, 15 deletions located in the region of exons 2-47 were milder BMD and intermediate patients, as the location of deletions was not the important region of the dystrophin gene.     

Antisense-induced multiexon skipping for Duchenne muscular dystrophy makes more sense

Dystrophin deficiency, which leads to severe and progressive muscle degeneration in patients with Duchenne muscular dystrophy (DMD), is caused by frameshifting mutations in the dystrophin gene. A relatively new therapeutic strategy is based on antisense oligonucleotides (AONs) that induce the specific skipping of a single exon, such that the reading frame is restored. This allows the synthesis of a largely functional dystrophin, associated with a milder Becker muscular dystrophy phenotype. We have previously successfully targeted 20 different DMD exons that would, theoretically, be beneficial for >75% of all patients. To further enlarge this proportion, we here studied the feasibility of double and multiexon skipping. Using a combination of AONs, double skipping of exon 43 and 44 was induced, and dystrophin synthesis was restored in myotubes from one patient affected by a nonsense mutation in exon 43. For another patient, with an exon 46-50 deletion, the therapeutic double skipping of exon 45 and 51 was achieved. Remarkably, in control myotubes, the latter combination of AONs caused the skipping of the entire stretch of exons from 45 through 51. This in-frame multiexon skipping would be therapeutic for a series of patients carrying different DMD-causing mutations. In fact, we here demonstrate its feasibility in myotubes from a patient with an exon 48-50 deletion. The application of multiexon skipping may provide a more uniform methodology for a larger group of patients with DMD.