克隆新基因cDNA全长的策略和方法

克隆新基因及获得其cDNA全长是现代生命科学中研究基因功能的重要前提。随着分子生物学技术的迅速发展，克隆新基因的技术也不断得到发展和完善，尤其是生物技术与信息技术的结合和应用，计算机克隆基因开始兴起。本文介绍几种近年常用的克隆新基因cDNA全长的方法，原理及其优缺点。     

一个新的蛋白激酶基因DYRK3的克隆及其特征分析

目的分离一个与人的蛋白激酶ＤＹＲＫ２高度同源新的蛋白激酶的全长ｃＤＮＡ，并推测其分类和功能。方法应用与人的蛋白激酶ＤＹＲＫ２高度同源的３′端部分ｃＤＮＡ序列为探针，筛选ｃＤＮＡ文库和ｇＤＮＡ文库，并进行氨基酸序列同源性分析和ＦＩＳＨ定位。结果从人的骨骼肌ｃＤＮＡ文库和睾丸ｃＤ－ＮＡ文库各分离到一个新的蛋白激酶的全长ｃＤＮＡ。骨骼肌来源的ｃＤＮＡ编码５８８个氨基酸的蛋白质，睾丸来源的ｃＤＮＡ编码５６８个氨基酸的蛋白质，前者第２７个氨基酸以后的序列与后者第７个氨基酸以后的序列完全一致。结论推测这两个ｃＤＮＡ是同一基因在骨骼肌组织和睾丸组织中的不同剪接本。由于该基因与人的ＤＹＲＫ２高度同源，故称之为ＤＹＲＫ３基因。ＤＹＲＫ３与丝氨酸／苏氨酸蛋白激酶酵母Ｙａｋ１，人和果蝇的Ｍｎｂ，人的Ｃｌｋ１等有较高的同源性，也与人的Ｃｄｋ２等其它丝氨酸／苏氨酸激酶有同源性。作者认为ＤＹＲＫ３是属于丝氨酸／苏氨酸蛋白激酶ＣＭＧＣ组Ｃｌｋ家族新的一员。该基因定位在１ｑ３２。     

人白细胞介素13cDNA的克隆及序列测定

用反转录－多聚酶链反应（ＲＴ－ＰＣＲ）技术从中国人外周血淋巴细胞中克隆了ＩＬ－１３ｃＤＮＡ，序列测定表明克隆的ＩＬ－１３ｃＤＮＡ含成熟的ＩＬ－１３蛋白全部编码，且存在编码第９８位Ｇｌｎ的密码子ＣＡＧ，这为进一步表达ＩＬ－１３并深入探究功能奠定了基础。     

轮状病毒1,2血清型VP7蛋白基因的扩增及其克隆

用聚合酶链反应扩增了轮状病毒Ｗａ株（第１血清型）和ＤＳ－１株（第２血清型）的全长ＶＰ７蛋白基因，利用两引物５＇末端的多接头位点，以ｐＵＣ１８质粒为载体构建了含两株ＲＶＶＰ７基因ｃＤＮＡ拷贝的重组体。经ＰＣＲ扩增制备得１～４血清型ＲＶＶＰ７基因高变区（５１－３９２核苷酸）￣（３２）Ｐ标记核酸探针，对重组质粒型别进行了Ｓｏｕｔｈｅｒｎ和斑点杂交鉴定，结果Ｗａ株ＶＰ７基因重组体只与１型探针呈强杂交信号，ＤＳ－１株重组体只与２型探针呈强杂交信号。     

parkin基因的一个新的点突变

目的：研究parkin基因外显子2-10点突变与散发性早发帕金森病发病的关系。方法：应用聚合酶链反应（polymerase chain reaction ，PCR）、琼脂糖电泳、单链构象多态性（single strand conformation polymorphism，SSCP）、DNA测序及限制性核酸内切酶酶切方法，检测了60例散发性早发帕金森病患者以及120名正常人外周血白细胞DNA的parkin基因外显子2-10点突变。结果：发现1例患者的parkin基因外显子2存在纯合突变（G237→C），限制性内切酶酶切证实，其它外显子未见突变，120名正常对照也未见突变。结论：parkin基因外显子存在点突变，可能与部分散发性早发帕金森病发病有关。     

cDNA微矩技术用于脓毒症小鼠肺组织中差异性表达基因的检测

目的本文在小鼠盲肠结扎一穿孔引起的混合感染性脓毒症模型上,首次采用了cDNA微矩阵(基因芯片)检测技术,研究脓毒症中肺组织在脓毒症后早期(6h)和晚期(12h)的基因表达的改变,以期从基因水平上揭示脓毒症性急性肺损伤的发病机制并为进一步寻找其新的防治手段打下基础.方法(1)小鼠混合感染性脓毒症的构建以小鼠CLP,构建混合感染性脓毒症模型.(2)CLP后肺组织中差异性表达基因的检测小鼠分为脓毒症组(A组)及假手术对照组(B组)分别于CLP后6h、12h摘取全肺,-70℃保存待测;检测采用上海联合基因公司提供的含2304个小鼠cDNA克隆杂交点的MCEG20S型基因芯片;各组不同时点的肺组织标本经RNA提取、mRNA纯化后,经逆转录反应分别合成标记以Cy5(A组)或Cy3(B组)荧光素的cDNA探针;各时点的A、B两组探针混合后分别与上述基因芯片杂交,经严格洗脱后用ScanArray5000型激光共聚焦扫描仪以两种不同波长分别对芯片进行扫描,得到芯片的荧光信号强度数据;以Image3.0软件分析各时点两组间的荧光值之比(R).R＞2.0为表达上调,R＜0.5为表达下调.结果(1)CLP后小鼠肺组织均出现典型的急性肺损伤的病理改变.24h生存率为40%;48h的生存率为7.5%;72h的生存率为5%.(2)在CLP后6h和12h,共筛选出80个与假手术对照组相比出现差异性表达的已知功能基因,其中表达上调和下调者各40个;CLP后6h有23个已知基因出现差异性表达,其中上调者12个,下调者11个;CLP后12h,有75个已知基因出现差异性表达,其中表达上调者39个,下调者36个;(3)对以上差异性表达基因按其功能予以聚类分析,发现脓毒症引起的急性肺损伤涉及到肺组织中一系列功能基因的表达改变,其中包括免疫相关基因、急时相反应与热休克反应相关基因、抗氧化反应基因、细胞骨架相关基因以及多种细胞代谢和信息传递相关基因.它们对脓毒症的病理生理的演变,可能起了重要的作用.(4)通过对本试验所发现的差异性表达的基因的生物信息学分析,遴选出了具有进一步研究价值或潜在治疗作用的基因.结论脓毒症中,一系列与炎性反应和细胞免疫相关的基因表达增高.同时热休克反应、抗氧化反应以及与细胞能量代谢和骨架结构相关的基因表达抑制,这可能是脓毒症病理生理改变进行性加重的原因.利用基因芯片技术可高效率、大规模地检测脓毒症、AL和MODS时基因表达的改变,高通量筛选与脓毒症发生和发展相关的基因,有利于从分子水平上澄清脓毒症的病理生理机制,比较不同的干预治疗效果,寻找新的治疗目标和治疗药物.     

普氏立克次体14kD蛋白基因的扩增与克隆

根据普氏立克次体弱毒株－Ｅ株１４ｋＤ表面蛋白基因的ＤＮＡ序列设计合成了一对寡核苷酸引物，二引物的５＇端分别加上了限制性内切酶ＥｃｏＲＩ和ＨｉｎｄⅢ酶切位点。采用此引物对成功地扩增了普氏立克次体强毒株－－Ｂｒｅｉｎｌ株（国际标准株）的１４ｋＤ表面蛋白基因，基因的分子大小为０．７２ｋｂ。扩增获得的基因ＤＮＡ经限制性内切酶ＨｉｎｄⅢ和ＥｃｏＲＩ酶切后与经相同酶切的质粒载体ｐＵＣ１９连接，转化受体大肠杆菌工程菌ＪＭ１０３，经酶切和ＤＮＡ斑点杂交鉴定，成功地克隆了扩增的普氏立克次体强毒株（Ｂｒｅｉｎｌ株）的１４ｋＤ表面蛋白基因。     

人类间隙连接蛋白CX58基因的克隆

目的 利用同源性分析，克隆定位新的人类间隙连接蛋白基因，并探讨该基因和遗传性耳聋的关系。方法 将小鼠Cx57基因的编码区与美国国家生物信息中心（National Center for Biotechnology Information,NCBI)的表达序列标签数据库（database of expressed sequence tags,dbEST)进行BLAST（basic local alignment search tool）分析，在得到的代表人类新基因的EST序列构建重叠群上设计引物CX58F1/CX58F2和CX58R1／CX58R2，分别与cDNA文库及Ready cDNA载体臂上引物行巢式聚合酶链反应（polymerase chain reaction,PCR)、cDNA末端快速扩增（rapid amplification of cDNA ends,RACE),获得cDNA后与大规模测序结果比较，定位该基因，并在常染色体显性遗传性耳聋家系中进行突变分析。结果 将利用同源性分析得到的9个人类新的EST，构建重叠群设计引物行巢式PCR、RACE，在肝、肾的Ready cDNA和胎盘cDNA文库中得到1个全长cDNA并命名为CX58。通过与大规模测序结果比较，将该基因定位于1p32.3-p34.1。12个常染色体显性遗传性耳聋家系中未检测到突变。结论 通过同源性分析，我们克隆定位了1个新的人类间隙连接蛋白基因CX58。该基因突变可能不是引起常染色体显性遗传性耳聋的常见原因或与该病无关。     

中国南京庚型肝炎病毒部分基因的克隆及cDNA序列分析

采用反转录聚合酶链反应（ＲＴＰＣＲ）从南京地区某输血后丙型肝炎患者血清中克隆出庚型肝炎病毒（ＨＧＶ）非结构区部分基因。序列分析结果表明：该序列与国外发表的庚型肝炎病毒ＨＧＵ４４４０２，ＨＧＵ４５９６６，ＨＧＵ３６３８０（ＧＢＶＣ）对应位置核苷酸序列同源性分别为８９０９％，９２１２％，８７２７％，与已报道的ＨＧＶ河北株序列同源性为９３９４％。对４０份输血后丙型肝炎血清和３０份非甲非乙非丙非丁非戊型肝炎血清进行了检测，ＨＧＶＲＮＡ阳性率分别为１０００％和６６７％。     

中国上海丁型肝炎病毒部分基因的克隆与序列分析

从我国上海无症状乙型肝炎病毒表面抗原（ＨＢｓＡｇ）携带者混合血清中提取ＲＮＡ，通过逆转录聚合酶链反应获得丁型肝炎病毒（ＨＤＶ）的长约３７０个碱基对的ｃＤＮＡ片段，将其克隆测序并与已知的ＨＤＶ各基因型代表株序列比较，结果表明，它与意大利株的同源性较高（９８．１％），与台湾株（Ｉａ型）及美国－１（Ｉｂ型）的同源性相近（９１．０％，９２．０％），与日本－１株（Ⅱ型）及秘鲁株（Ⅲ型）的同源性为７９．３％（     

唇腭裂相关基因研究进展

唇腭裂是一种常见的先天性畸形,其病因非常复杂,目前倾向认为是由多种基因和环境因素共同作用的结果。常见的引起唇腭裂相关的基因有TGFA,TGFβ3, BCL3, F13A等;环境因素在唇腭裂发生中的遗传修饰作用也很重要,主要的环境激发因素包括致畸因子（如烟草、酒精、糖皮质激素等）、感染和营养缺乏。基于基因打靶技术建立的鼠基因敲除模型很好地模拟了人类疾病的表现型,成为研究唇腭裂的一种强有力手段。     

A novel mutation in the PHF8 gene is associated with X-linked mental retardation with cleft lip/cleft palate

Recently, two truncating mutations in the PHF8 (plant homeodomain finger protein 8) gene have been found to cause X-linked mental retardation associated with cleft lip/cleft palate (CL/P). One of the truncating mutations was found in the original family with Siderius-Hamel CL/P syndrome where only two of the three affected individuals had mental retardation (MR) with CL/P and one individual had mild MR. The second mutation was present in a family with four affected men, three of whom had MR and CL/P, while the fourth individual had mild MR without clefting. Here, we report a novel nonsense mutation (p.K177X) in a male patient who has MR associated with CL/P. The mutation results in a truncated PHF8 protein lacking the Jumonji-like C terminus domain and five nuclear localization signals. Our finding further supports the hypothesis that the PHF8 protein may play an important role in cognitive function and midline formation.     

Gene/environment causes of cleft lip and/or palate

Craniofacial anomalies, and in particular cleft lip and palate, are major human birth defects with a worldwide frequency of 1 in 700 and substantial clinical impact. A wide range of studies in developmental biology has contributed to a better knowledge of how both genes and environmental exposures impact head organogenesis. Specific causes have now been identified for some forms of cleft lip and palate, and we are at the beginning of a time in which the common nonsyndromic forms may also have specific etiologies identified. Mouse models have an especially important role in disclosing cleft etiologies and providing models for environmental cotriggers or interventions. An overview of the gene-environment contributions to nonsyndromic forms of clefting and their implications for developmental biology and clinical counseling is presented.     

Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate

We investigated the prevalence of mutations in the PHD finger protein 8 (PHF8) gene in X-linked mental retardation (XLMR) and facial cleft starting from the original cohort of 7712 patients operated on since 1 January 1950 for cleft lip/cleft palate in the Cleft Centre at the Helsinki University Hospital. From this nationwide material, 18 patients including one family with two male patients with cleft lip/cleft palate and unknown cause of mental retardation (MR) were sequenced for the coding regions and splice sites of the PHF8 gene. A novel missense mutation c.836C>T of the PHF8 gene was identified in a Finnish family with multiple-affected male patients. The mutation resides in exon 8 and changes phenylalanine to serine (F279S) in the functionally important Jmonji C domain of the protein. The clinical phenotype of the male patients was characterized by mild MR, mild dysmorphic features, unilateral cleft lip and cleft palate in one and bilateral cleft lip and cleft palate in the other sibling. The mutation was not present in 200 anonymous blood donors (approximately 300 X-chromosomes). To our knowledge, F279S is the third mutation of the PHF8 gene identified so far.     

Robin sequence without cleft palate: Genetic diagnoses and management implications

Robin sequence (RS), the triad of micrognathia, glossoptosis, and airway obstruction, is a major cause of respiratory distress and feeding difficulties in neonates. Robin sequence can be associated with other medical or developmental comorbidities in ~50% of cases (“syndromic” RS). As well, RS is variably associated with cleft palate (CP). Previous studies have not investigated differences in clinical characteristics of children with RS based on presence or absence of CP. We retrospectively reviewed 175 children with RS and compared genetic diagnoses, medical and developmental comorbidities, severity of airway obstruction, and feeding outcomes between those with and without CP. Strikingly, 45 of 45 (100%) children with RS without CP were classified as syndromic due to presence of comorbidities unrelated to RS, while 83 of 130 (64%) children with RS with CP were classified as syndromic. Among 128 children with syndromic RS, there were no differences in severity of airway obstruction, surgical intervention rate or type, or feeding outcome at 12 months based on CP status. Our findings support the conclusion that the pathogenesis of RS without CP is distinct from RS with CP and more likely to cause additional medical or developmental problems. Alternatively, children with RS without CP and without additional anomalies present may be under recognized.     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

Objective To study the association of the A2756G polymorphism of the methionine synthase (MS) gene with nonsyndromie cleft lip with or without cleft palate (NSCL/P) in Chinese. Methods Ninety-seven NSCL/P case-parent triads were selected as the case group. One hundred and four healthy subjects and their biological parents were selected as control group. For all subjects the A2756G polymorphism of the MS gene was examined by PCR-RFLP method. Results There was no statistical difference in genotype and allele frequencies for MS A2756G variants among family members between case group and control group. The GG genotype was not detected in the offsprings and mothers. The odds ratio and confidence interval of genotype AG in offspring, father and mother were 1.78(0.74-4.34), 0.80(0. 36-1.79) and 1.26(0. 54-2.93) respectively. The odds ratio and confidence interval of allele G in offspring, father and mother were 1.70(0.78-3.73), 0. 88(0. 49-1. 75) , and 1.23(0.59-2.60) respectively. The G allele did not increase the risk of NSCL/P. Transmission disequilibrium test (TDT) analysis yielded no evidence of linkage disequilibrium (χ2=0.034,P>0. 05). The results of haplotype-based haplotype relative risk (HHRR) analysis (χ2=0.03,P>0.05) and family-based association tests (FBAT) (Z=0. 186, P> 0.05) failed to show association between the MS A2756G variant and the risk of NSCL/P. Conclusion The A2756G polymorphism of the MS gene was not associated with NSCL/P in Chinese in the present study.     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

Objective To study the association of the A2756G polymorphism of the methionine synthase (MS) gene with nonsyndromie cleft lip with or without cleft palate (NSCL/P) in Chinese. Methods Ninety-seven NSCL/P case-parent triads were selected as the case group. One hundred and four healthy subjects and their biological parents were selected as control group. For all subjects the A2756G polymorphism of the MS gene was examined by PCR-RFLP method. Results There was no statistical difference in genotype and allele frequencies for MS A2756G variants among family members between case group and control group. The GG genotype was not detected in the offsprings and mothers. The odds ratio and confidence interval of genotype AG in offspring, father and mother were 1.78(0.74-4.34), 0.80(0. 36-1.79) and 1.26(0. 54-2.93) respectively. The odds ratio and confidence interval of allele G in offspring, father and mother were 1.70(0.78-3.73), 0. 88(0. 49-1. 75) , and 1.23(0.59-2.60) respectively. The G allele did not increase the risk of NSCL/P. Transmission disequilibrium test (TDT) analysis yielded no evidence of linkage disequilibrium (χ2=0.034,P>0. 05). The results of haplotype-based haplotype relative risk (HHRR) analysis (χ2=0.03,P>0.05) and family-based association tests (FBAT) (Z=0. 186, P> 0.05) failed to show association between the MS A2756G variant and the risk of NSCL/P. Conclusion The A2756G polymorphism of the MS gene was not associated with NSCL/P in Chinese in the present study.     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

Objective To study the association of the A2756G polymorphism of the methionine synthase (MS) gene with nonsyndromie cleft lip with or without cleft palate (NSCL/P) in Chinese. Methods Ninety-seven NSCL/P case-parent triads were selected as the case group. One hundred and four healthy subjects and their biological parents were selected as control group. For all subjects the A2756G polymorphism of the MS gene was examined by PCR-RFLP method. Results There was no statistical difference in genotype and allele frequencies for MS A2756G variants among family members between case group and control group. The GG genotype was not detected in the offsprings and mothers. The odds ratio and confidence interval of genotype AG in offspring, father and mother were 1.78(0.74-4.34), 0.80(0. 36-1.79) and 1.26(0. 54-2.93) respectively. The odds ratio and confidence interval of allele G in offspring, father and mother were 1.70(0.78-3.73), 0. 88(0. 49-1. 75) , and 1.23(0.59-2.60) respectively. The G allele did not increase the risk of NSCL/P. Transmission disequilibrium test (TDT) analysis yielded no evidence of linkage disequilibrium (χ2=0.034,P>0. 05). The results of haplotype-based haplotype relative risk (HHRR) analysis (χ2=0.03,P>0.05) and family-based association tests (FBAT) (Z=0. 186, P> 0.05) failed to show association between the MS A2756G variant and the risk of NSCL/P. Conclusion The A2756G polymorphism of the MS gene was not associated with NSCL/P in Chinese in the present study.     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

Objective To study the association of the A2756G polymorphism of the methionine synthase (MS) gene with nonsyndromie cleft lip with or without cleft palate (NSCL/P) in Chinese. Methods Ninety-seven NSCL/P case-parent triads were selected as the case group. One hundred and four healthy subjects and their biological parents were selected as control group. For all subjects the A2756G polymorphism of the MS gene was examined by PCR-RFLP method. Results There was no statistical difference in genotype and allele frequencies for MS A2756G variants among family members between case group and control group. The GG genotype was not detected in the offsprings and mothers. The odds ratio and confidence interval of genotype AG in offspring, father and mother were 1.78(0.74-4.34), 0.80(0. 36-1.79) and 1.26(0. 54-2.93) respectively. The odds ratio and confidence interval of allele G in offspring, father and mother were 1.70(0.78-3.73), 0. 88(0. 49-1. 75) , and 1.23(0.59-2.60) respectively. The G allele did not increase the risk of NSCL/P. Transmission disequilibrium test (TDT) analysis yielded no evidence of linkage disequilibrium (χ2=0.034,P>0. 05). The results of haplotype-based haplotype relative risk (HHRR) analysis (χ2=0.03,P>0.05) and family-based association tests (FBAT) (Z=0. 186, P> 0.05) failed to show association between the MS A2756G variant and the risk of NSCL/P. Conclusion The A2756G polymorphism of the MS gene was not associated with NSCL/P in Chinese in the present study.