基于CDS..join特征域的Exon/Intron数据库的构建

基因进化的研究和重构通常是在序列水平上进行的,包括比对它们的基因序列或蛋白序列.而对基因外显子/内含子结构的分析能够提供更多有价值的信息,比如绘制更为可靠的系统发生图谱,或更精确地阐明内含子的进化.为此,本文设计了相应的Perl脚本程序来提取、比较和搜索基因说明文档中CDS..join特征域的Exon/Intron结构.通过该方法,可构建相关物种的Exon/Intron数据库(EID),其主要内容包括内含子的相位,Exon或Intron的数量和大小,剪接位点的模式以及选择性剪接(Alternative splicing,AS)的相关信息.

人类基因组非冗余Exon/Intron数据库的构建

以Homo.sapiensRefSeq作为原始数据库来构建EID(Exon/Intron Database)可以克服GenBank所带来的冗余问题.通过分析RefSeq基因组数据库中每个CDS(Coding Sequence,编码序列),获得构建EID的相关的数据(基因的定义、基因标识符、基因序列、蛋白质标识符、蛋白质序列、外显子和内含子的数量、大小、总数、非翻译区(UTR)内含子、内含子相位、内含子剪切位点模式).结果表明,人类24条染色体(22条常染色体和2条性染色体,共计2 870 827355 bps)中含有32 157个基因标识符(gene blocks),其中7 398个基因为假基因,4 014个基因发生了可变剪切(Al-ternative Splicing,AS),15 533个基因含有CDS内含子,765个基因含有UTR内含子,2 585个基因不含有内含子,其他的为异常基因.

达可替尼与吉非替尼一线治疗EGFR Exon19/21突变型晚期非小细胞肺癌的疗效对比

目的对比达可替尼与吉非替尼一线治疗EGFR Exon19/21突变型晚期非小细胞肺癌的疗效。方法收集108例表皮生长因子受体(epidermal growth factor receptor,EGER)突变型晚期非小细胞肺癌(non-small cell lung cancer,NSCLC)患者资料,依据治疗方法的不同将患者分为2组,达可替尼组58例,吉非替尼50例。统计2组疗效。结果2组基线特征比较差异均无统计学意义(P>0.05)。达可替尼组与吉非替尼组近期疗效比较,差异均无统计学意义(P>0.05)。随访截止2023年6月,2组患者均完成随访,无脱落病例。达可替尼组中位PFS长于吉非替尼组(12.6 vs 8.5个月,χ^(2)=34.009,P<0.001)。达可替尼组患者中位OS为23.1个月,吉非替尼组患者中位OS为16.3个月,2组间OS差异无统计学意义(χ^(2)=2.123,P=0.158)。2组患者不良反应发生情况比较,差异均无统计学意义(P<0.05),但是达可替尼组Ⅰ度、Ⅱ度胃肠道反应以及Ⅲ度、Ⅳ度痤疮发生率略高。结论达可替尼与吉非替尼一线治疗EGFR Exon19/21突变型晚期非小细胞肺癌的疗效相似,但是达可替尼组PFS更具优势,而吉非替尼相较达可替尼安全性略高。

牦牛和普通牛DRB1*Intron1-exon2序列变异分析

为揭示牦牛抗逆性及抗病育种积累更多的分子遗传学资料,通过检测DRB1基因在牦牛和普通牛群体中的变异,分析该基因检测区域遗传参数。以甘南牦牛、青海牦牛、天祝白牦牛、大通牦牛和普通牛为研究对象。应用PCR-SSCP方法检测BoLA-DRB1基因第1内含子及第2外显子部分序列多态性。DRB1基因第1内含子区检测到4处SNPs及1处插入/缺失突变,第2外显子区检测到17处SNPs,两区域均表现为高度多态;单倍型连锁分析发现21种intron 1-exon 2单倍型组型且存在单倍型连锁不平衡现象,A-A1、A-B1、B-A1和B-B1单倍型在牦牛和普通牛中频率较高;聚类分析表明,牦牛DRB1基因第2外显子区碱基序列与普通牛及山羊的同源性最高,系统进化情况与它们亲缘关系远近一致。牦牛和普通牛BoLA-DRB1基因第1内含子及第2外显子多态性丰富,可作为牦牛和普通牛BoLADRB1的遗传标记。

Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ) Marker and Its Application in Construction of Upland Cotton Linkage Map

To develop a new DNA maker, which could be used in genetic diversity analysis and genetic map construction in plants, IT-ISJ （intron targeted intron-exon splice junction） primer combinations, which were designed according to the intronexon splice junction conserved sequences, were used to construct cotton genetic linkage map in the present study. 49 out of 704 IT-ISJ primer combinations showed polymorphism between upland cotton high quality cultivar Yumian 1 and multiple dominant gene line T586, and the polymorphic primer combinations accounted for 7.0% of total primer combinations. 49 IT-ISJ primer combinations were used to genotype 270 F2：7 recombinant inbred lines developed from （Yumian 1 × T586） F2, and 58 IT-ISJ loci were obtained. 58 IT-ISJ, together with 150 SSR and 8 morphological loci, were used to conduct linkage analysis, and a linkage map including 22 linkage groups and 113 loci （49 IT-ISJ, 62 SSR, and 2 morphological loci） was constructed. The linkage map covered 714.5 cM with an average interval of 6.3 cM between two markers, accounting for 16.1% of cotton genome. The present study demonstrated that the polymorphism of IT-ISJ marker is high, and it could be effectively applied in plant genetic map construction.

Investigation on the Interface between Exons and Introns in the Genomic DNA of Arabidopsis thaliana in the Phase Space

In this study,three weight vectors L1,L2 and L3 were set.After calculating the probability of three bases in the exons or introns in the genomic DNA of Arabidopsis thaliana,64-dimensional vector P was obtained.Dot products of P vector and three weight vectors were the feature coordinates for the exons and introns in 3-dimensional phase space.The expression for the interface between the exons and the introns in the genomic DNA of Arabidopsis thaliana in 3-dimensional phase space was established,which could be used to distinguish the exons and the introns in the genomic DNA of Arabidopsis thaliana with an accuracy higher than85%in 3-dimensional phase space.

Analysis and prediction of exon, intron, intergenic region and splice sites for A. thaliana and C. elegans genomes

Although a great deal of research has been undertaken in the area of the annotation of gene structure, predictive techniques are still not fully developed. In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. The results show that overall predicted accuracies are 91.1% and 88.4%, respectively for A. thaliana and C. ele-gans genome. Subsequently, based on the po-sition frequencies of four kinds of bases in regions near intron/coding exon boundary, initia-tion and termination site of translation, 12 position parameters are selected as diversity source. And three kinds of the coding exons are predicted by use of the LIDA. The predicted successful rates are higher than 80%. These results can be used in sequence annotation.

Determination of the Exon-Intron Boundary in a Zinc-finger Gene (ZNF191) by Bubble PCR

A rapid and accurate method was used to identify the exon intron boundaries in a novel zinc finger gene ZNF191. Genomic DNAs containing the sequence of ZNF191 cDNA were digested with proper restriction enzymes and then ligated to an annealed bubble linker. The ligation product was used as the template to carry out PCR with the primers of ZNF191 cDNA and the bubble linker. Then the PCR products were sequenced to determine the exon intron boundaries. The results show that the zinc finger gene(ZNF191) has 4 exons and 3 introns. It was further confirmed by the sequencing data of genomic DNA of the gene ZNF191.

Comparative Analysis of the Exon-Intron Structure in Eukaryotic Genomes

The exon numbers and lengths vary in different eukaryotic species. With increasing completed genomic sequences, it is indispensable to reanalyze the gene organization in diverse eukaryotic genomes. We performed a large-scale comparative analysis of the exon-intron structure in 72 eukaryotic organisms, including plants, fungi and animals. We confirmed that the exon-intron structure varies massively among eukaryotic genomes and revealed some lineage-specific features of eukaryotic genes. These include a teleost-specific exon-intron structure pattern, relatively small introns and large exons in fungi and algae, and a gradual expansion of introns in vertebrates. Furthermore, the conservation analysis of exon-intron boundaries indicates that several bases near splice site junctions are different in introns with variable length among different species. After comparison, we identified a trend showing increases in intron densities and lengths in diverse species from fungi, plants, invertebrates to vertebrates, while it was the opposite in relation to exon lengths. The statistical properties of eukaryotic genomic organization suggest that genome-specific features are preserved by diverse evolutionary processes, which paves way for further research on the diversification of eukaryotic evolution.

Targeted editing of intronic-splicing silencer enhancement of SMN2 Exon 7 inclusion by CRISPR/Case 9

Spinal muscular atrophy(SMA)is an autosomal recessive hereditary neuromuscular disease.Exon 7 and 8 of survival of motor neuron 1(SMN1)gene or only exon 7 homology deletion leads to the failure to produce a full-length SMN gene.The copy number of SMN2 gene with high homology of SMN1 affects the degree of disease and was the target gene for targeting therapy,in which splicing silencer in intron 7 was the key to suppress the inclusion of exon 7.In this study,we projected to use CRISPR/Case 9 for the targeted editing of intronic-splicing silencer(ISS)sequence to promote the inclusion of SMN2 exon 7 and increase the production of SMN2 full-length(FL)gene expression.It happens that there was a protospacer adjacent motif(PAM)at one end of the ISS sequence according to the design of sgRNA.The recombinant vector of sgRNA HSMN2 CRISPR/Case 9 was constructed and transfected into HEK293 cells.Sequencing results showed that the ISS sequence could be edited accurately and targeting in the predicted direction,in which deleting small fragments,inserting small amounts and mutation.Quantitative analysis of RT-PCR products by restriction enzyme of DdeI digestion showed that the FL of SMN2 increased by 8%(P<0.05).In the primary cultured chondrocytes of SMA mice,in which sgRNA HSMN2 CRISPR/Case9 recombinant vector transfection could increase the SMN2 FL gene by 23%(P<0.05)and significantly improve SMN protein levels(P<0.05).CRISPR/Case 9 is an effective tool for gene editing and therapy of hereditary diseases,but it is rarely reported in the treatment of SMA diseases.This study shows that CRISPR/Case 9 was first used for the precision target of ISS sequence editing,which can effectively promote the production of SMN2 FL gene expressions,in which there was an important clinical reference value.

Intron Retention Fine-Tunes the Resistance of the Rice Mutant pls4 to Rice Sheath Blight(Rhizotonia solani AG I.1a)

OsPLS4 encodes aβ-ketoacyl carrier protein reductase(KAR).The role of OsPLS4 in rice sheath blight(Rhizoctonia solani)remains unclear.Our preliminary studies showed that premature leaf senescence mutants(pls4)were highly susceptive to sheath blight in the early stage of rice development.To explore the role of this gene in the development of rice sheath blight,the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq.The results revealed 2,569 differentially expressed genes(DEGs).The down-regulated genes were significantly enriched in the defense response-related biological processes.These down-regulated genes included the chitinase genes and WRKY genes,which were significantly changed in pls4 mutants.Furthermore,467 genes induced significant alternative splicing(AS)events.Among them,intron retention(IR)affected gene expression levels and functions of the vitamin B6(VB6)metabolism pathway related to sheath blight.This result suggests that IR plays an important role in the sheath blight resistance of mutant pls4.Together,these results indicate that pls4 could be involved in the biological process of sheath blight via DEGs and the fine-tuning of IR.The present study provides a molecular basis for further investigation of the resistance of rice to sheath blight.

早发型帕金森病家系相关基因的筛查和危险度分析

目的:通过早发型帕金森病(early‑onset Parkinson’s disease,EOPD)遗传家系成员的高通量基因筛查,发现疾病相关突变位点并检测其在人群中对疾病的影响。方法:本研究对早发型PD遗传家系中19名成员进行单核苷酸多态性芯片检测和全外显子基因分型,并通过对家系外散发人群58人进行测序验证,筛选具有较高风险的突变位点。结果:芯片连锁分析发现3个染色体区段、全外显子测序和共表达分析筛选出24个可能与疾病关联的基因。其中5个位点基因型与患病结局之间的Spearman相关系数r>0.6且P<0.05,表示具有关联。通过家系外散发患者测序验证,Ddx56基因(OR=10.923)和Aspn基因(OR=8.198)的突变对患病结局产生显著影响(P<0.05)。结论:本研究通过临床患者进行多层次突变位点筛查分析,发现外显子区域的5个突变基因Pdxdc1、Ddx56、Aspn、Rbm28和Shisa9可能与帕金森病密切相关。

ABO血型基因外显子1上新变异的鉴定

目的:应用血清学和分子生物学方法鉴定1例ABO正反定型不一致患者的血型,并探讨其遗传学特点。方法:采用试管法鉴定该患者的ABO表型,荧光PCR法测定患者及其父母的ABO血型基因型,并对ABO基因7个外显子进行直接测序分析。结果:本例患者血清学初步鉴定为Bel亚型;基因分型检测患者及其父亲的基因型为B/O1,其母亲的基因型为O1/O1;测序发现在患者及其父亲ABO基因外显子1上有新的c.16_17delins TGTTGCA杂合变异。结论:外显子1上新的变异导致该患者ABO血型出现Bel亚型,并具有遗传性。

扁桃体鳞状细胞癌临床病理分析及全外显子测序分析

目的探讨扁桃体鳞状细胞癌(tonsil squamous cell carcinoma,TSCC)的临床病理学特征、全外显子突变和肿瘤突变负荷(tumor mutational burden,TMB)。方法回顾性分析10例TSCC临床病理特征,采用EnVision两步法检测CK(AE1/AE3)、CK5/6、p63、p40、p16和Ki67等蛋白的表达,并对其中3例TSCC病例行全外显子组测序及TMB分析。结果10例患者中,男性6例,女性4例,年龄43~76岁,光镜下癌细胞呈巢状和不规则条索状浸润至隐窝上皮下,伴有粉刺样坏死,见细胞间桥及多少不一的角化,异型性明显,核分裂象易见。随访6~45个月,9例存活。免疫表型:CK(AE1/AE3)、CK5/6、p63和p40均阳性,3例p16弥漫强阳性,Ki67增殖指数40%~90%。3例TSCC的全外显子组测序结果显示ARID1B、LRP6等为常见的癌症易感基因,WDFY4、ZFHX4基因表现出较高的突变比例,均为3/3。TMB分析结果显示3例突变中1例TMB值>9 mut/Mb。结论TSCC早期症状不明显,容易漏诊误诊。全外显子组测序结果显示WDFY4、ZFHX4基因存在较高的突变率。TMB结果提示TSCC部分患者可在免疫治疗中获益。

赛沃替尼治疗MET基因突变非小细胞肺癌的药物浓度与疗效和不良反应的关系

目的:探讨药物浓度与疗效和不良反应之间的关系,了解赛沃替尼治疗MET14外显子跳跃突变晚期非小细胞肺癌患者的疗效和安全性。方法:回顾性分析2018年4月至2019年9月北京大学肿瘤医院收治的携带MET14外显子跳跃突变,并且接受赛沃替尼治疗的16例局部晚期或转移性非小细胞肺癌患者的临床资料及其血浆药物浓度,评估赛沃替尼治疗的疗效和安全性,分析药物浓度与疗效及不良反应的相关性。随访患者的无进展生存期(progression-free survival,PFS)和总生存期(overall survival,OS),采用Kaplan-Meier法计算中位PFS和OS。结果:16例患者中男性9例(56.3%),年龄范围51~84岁。肺癌病理类型包括:腺癌11例,肉瘤样癌5例,鳞癌1例。赛沃替尼的客观缓解率为50.0%(8/16),疾病控制率达到87.5%(14/16)。评效达到部分缓解患者和未达到者相比,赛沃替尼的药物谷浓度分别为77.2 ng/mL和146.7 ng/mL(P=0.06)。治疗中出现过2级以上不良反应的患者和仅出现过1级不良反应者,其药物谷浓度分别为116.5 ng/mL和93.2 ng/mL(P=0.59)。所有患者的中位PFS为8.5个月,中位OS为14.1个月。结论:赛沃替尼治疗MET基因突变非小细胞肺癌的效果较好,不良反应可耐受。常规用药剂量下,赛沃替尼的血浆药物谷浓度与疗效可能存在一定负相关,但药物浓度与不良反应的程度无明显相关性。

NOTCH3基因C260S位点突变导致CADASIL的临床和影像学特征分析

目的探讨NOTCH3基因第5外显子C260S位点突变导致的伴有皮层下梗死和白质脑病的常染色体显性遗传性脑动脉病(cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy,CADASIL)家系的临床和影像学特征。方法选取2021年12月首都医科大学附属北京同仁医院来自同一家庭的CADASIL患者,对所有患者进行NOTCH3基因测序,回顾性分析患者的临床表现和头颅影像学特征。复习既往文献报道的导致同一位置氨基酸改变的其他突变类型的临床及影像学特征。结果4名家庭成员中,包括先证者(46岁,女)及其两个姐姐(分别为48岁和50岁)和女儿(18岁)。先证者及其父亲、两个姐姐都有偏头痛病史,其中大姐有记忆力减退;先证者患有脑梗死及伴有视觉先兆的偏头痛;先证者女儿体健;先证者父亲因脑梗死去世。4名家庭成员均存在C260S位点的NOTCH3基因突变。既往文献无此位点突变的报道,先证者头颅MRI示右侧脑桥亚急性梗死,颞叶、脑室周围及脑干异常高信号改变,其大姐脑桥可见腔隙性梗死灶。结论NOTCH3基因第5外显子c.778T>A(p.C260S)的罕见突变导致的CADASIL发病时间早,早期会出现认知障碍。合并偏头痛的脑干梗死患者,需警惕CADASIL的可能。

西农萨能羊乳腺脂肪酸合酶基因exon 9-15的克隆与序列分析

【目的】山羊FAS基因exon 9-15编码的乙酰/丙二酸单酰基转移酶(acetyl-CoA and malonyl-CoA transacylases,AT/MT)区域对山羊乳短、中链脂肪酸的合成起重要调控作用。本研究针对西农萨能羊乳腺FAS基因exon 9-15进行克隆和序列分析。【方法】以处于泌乳期28d的西农萨能羊乳腺组织mRNA反转录的cDNA为模板,通过RT-PCR方法首次扩增出西农萨能羊乳腺FAS基因exon 9-15的cDNA序列全长及exon 8的3′端和exon 16的5′端部分cDNA序列(GenBank收录号为DQ915966),并对其进行了同源性分析和功能预测。【结果】克隆片段全长1449bp,其中包括exon 9-15共1388bp、exon 8的3′端9bp和exon 16的5′端52bp,编码483个氨基酸,包含编码的AT/MT区域951bp(454～1404nt);西农萨能羊乳腺FAS基因exon 9-15与牛(NM_001012669),人(NM_004104),大鼠(NM_017332)和鸡(NM_205155)核苷酸序列相似度分别为95%、85.7%、82.7%、73.2%,氨基酸相似度分别为92.9%、77.7%、82.3%、64.7%;exon 10较其它物种缺失1个氨基酸。【结论】克隆获得西农萨能羊FAS基因片段全长1449bp,外显子9-15大小分别为463、185、190、95、135、204和116bp;核苷酸及氨基酸序列与牛相应序列的同源性均高于其它物种;AT/MT区域的活性位点在各物种间均为高度保守的丝氨酸,但西农萨能羊exon 10较其它物种缺失1个氨基酸,这可能对AT/MT区域的空间构象及其生理功能产生重要影响。本研究为西农萨能羊FAS基因cDNA全长克隆以及基因功能研究奠定了重要基础。

中国大陆野猪SLA DRB基因exon2的序列变异分析

本文基于135头野猪样本中检测到的15种SLA DRB基因exon 2序列的遗传变异分析,探讨DRB基因在不同地理区域中自然选择的变化特征。研究发现DRB基因exon 2抗原结合位点的非同义替换率为同义替换率的2.95倍,表明该位点受到平衡选择的强烈作用。在系统发生分析中,在基于核苷酸序列构建的NJ树中,野猪DRB位点的15种等位基因全部聚为一枝,没有发现跨种多态现象;而在基于氨基酸序列构建的系统发生树中,野猪SLA-DRB*nnu6和人DRB基因exon 2片段聚在一起,这种氨基酸残基的高度相似可能是由于自然选择压力下产生的趋同。野猪DRB基因exon 2的序列多态性分析表明,东北野猪基因多态性低于四川野猪和华南野猪,这可能与不同气候条件和地理环境下的寄生虫等因素对SLA等位基因变异的影响存在差异有关。

GHR基因exon 9和exon 10多态性与西农萨能奶山羊产奶性能的相关分析

针对GHR基因exon 9和exon 10设计了2对引物,采用PCR-SSCP技术检测该基因这2个位点在西农萨能羊群上的单核苷酸多态性,同时研究其对产奶性能的影响。结果表明:exon 9具有多态,exon 10不存在多态性。Exon 9位点在西农萨能山羊中检测到NN型和NT型,纯化测序发现有1个SNP位点,NN型与NT型相比在该片段第241 bp处有1个G→T的突变;NN和NT基因型之间产奶量的最小二乘均值差异显著(P<0.05):NN基因型在各胎次产奶量和平均产奶量等指标上均好于NT基因型,其中在第3胎的产奶量和第4胎产奶量2项指标上都达到显著水平(P<0.05)。研究结果提示:GHR基因exon 9对奶山羊产奶量有显著影响,因此认为GHR基因exon 9位点可作为奶山羊高产奶量的标记辅助选择的有效分子标记。

a-1,3-N-乙酰半乳糖胺转移酶基因EXON 7突变形成A311血型基因亚型

本研究对1例产生抗A抗体的血清学正反定型不符的A血型标本进行血型血清学分析及基因分析,以了解其分子基础。采用试管法进行血型血清学的检测,采用PCR-SSP对A基因进行扩增分析,采用Sanger测序法对A血型糖基转移酶基因进行测序分析。结果表明:血清学正反定型不符,初定为A亚型;PCR-SSP扩增检测结果有O、A血型基因的存在;对ABO基因第6外显子测序发现存在c.261delG,显示有O基因;对A、O基因第7外显子进行特异性扩增测序分析显示,在A单倍型基因第7外显子出现c.467 C>T、c.626 G>A的突变,在O单倍型基因第7外显子出现c.646T>A、681G>A、771C>T、829G>A等突变。结论:该献血者在A基因第7外显子的c.626G>A是新的等位基因突变,c.467 C>T是SNP;新突变的GenBank序列号是KC690281,被BGMUT命名为1个新的A等位基因亚型A311。