The Minor T Allele of the Single Nucleotide Polymorphism rs13360222 Decreases the Activity of the HAVCR2 Gene Enhancer in a Cell Model of Human Macrophages

Molecular Biology - The TIM-3 receptor, encoded by the Hepatitis A Virus Cellular Receptor 2 (HAVCR2) gene, is an immune checkpoint and plays an important role in preventing the development of...     

PRPS2基因启动子区的单核苷酸多态性(英文)

人类基因组变异主要以单核苷酸多态性 (SNPs)为主 .采用多荧光标记的PCR单链构象多态性分析法 (MF PCR SSCP)对磷酰核糖焦磷酸合成酶亚基Ⅱ (PRPS2 )基因启动子区的序列进行了SNP的筛选 ,对筛选到的阳性片段进行序列分析以确定SNP的类型及位置 .在 1 5kb的启动子区发现了 2个SNP (- 10 79t c ,- 1110a g) .研究结果为PRPS2基因SNPs的数据库提供了新的信息 .     

E-钙粘蛋白基因启动子区域单核苷酸基因多态性(-347G→GA)和大肠癌遗传易感性的联系

目的:探讨E-钙粘蛋白基因(CDH1)启动子区域-347G→GA单核苷酸基因多态性(single nucleotide polymorphism,SNP)和中国地区散发大肠癌(colorectal cancer,CRC)人群遗传易感性的联系.方法:以中国地区大肠癌病人群为研究基础,同时建立无肿瘤家族史以及其它遗传性疾病史的正常对照组,进行病例对照研究,采用聚合酶链反应一限制性片段长度多态性技术(poly-merase chain reaction-restriction fragment length polymorphism,PCR-RFLP)行目的基因的多态性测定.结果:正常对照组和大肠癌组的目的基因型分布频率并无统计学差异(x2检验,P=0.246),而近端大肠癌患者中GA基因型(GA/GA杂合子和GA/GA纯合子)比例明显高于对照组(OR=1.773,95%CI=1.174-2.679,P=0.007),同时低分化大肠腺癌GA基因型比例也明显高于对照组(OR=2.623,95%CI=1.326-5.191,P=0.007).结论:CDHl启动子区域-347G→GA单核苷酸基因多态性中GA基因型可能增加近端大肠癌以及低分化腺癌的发病风险.     

The Type 2 Diabetes Associated Minor Allele of rs2237895 KCNQ1 Associates with Reduced Insulin Release Following an Oral Glucose Load

Background

Polymorphisms in the potassium channel, voltage-gated, KQT-like subfamily, member 1 (KCNQ1) have recently been reported to associate with type 2 diabetes. The primary aim of the present study was to investigate the putative impact of these KCNQ1 polymorphisms (rs2283228, rs2237892, rs2237895, and rs2237897) on estimates of glucose stimulated insulin release.

Methodology/Principal Findings

Genotypes were examined for associations with serum insulin levels following an oral glucose tolerance test (OGTT) in a population-based sample of 6,039 middle-aged and treatment-naïve individuals. Insulin release indices estimated from the OGTT and the interplay between insulin sensitivity and insulin release were investigated using linear regression and Hotelling T2 analyses.Applying an additive genetic model the minor C-allele of rs2237895 was associated with reduced serum insulin levels 30 min (mean±SD: (CC) 277±160 vs. (AC) 280±164 vs. (AA) 299±200 pmol/l, p = 0.008) after an oral glucose load, insulinogenic index (29.6±17.4 vs. 30.2±18.7vs. 32.2±22.1, p = 0.007), incremental area under the insulin curve (20,477±12,491 vs. 20,503±12,386 vs. 21,810±14,685, p = 0.02) among the 4,568 individuals who were glucose tolerant. Adjustment for the degree of insulin sensitivity had no effect on the measures of reduced insulin release. The rs2237895 genotype had a similar impact in the total sample of treatment-naïve individuals. No association with measures of insulin release were identified for the less common diabetes risk alleles of rs2237892, rs2237897, or rs2283228.

Conclusion

The minor C-allele of rs2237895 of KCNQ1, which has a prevalence of about 42% among Caucasians was associated with reduced measures of insulin release following an oral glucose load suggesting that the increased risk of type 2 diabetes, previously reported for this variant, likely is mediated through an impaired beta cell function.     

人SATB1基因5′上游序列的转录激活功能分析

在对人SATB1基因进行生物信息学分析的基础上 ,采用PCR技术 ,扩增人基因组DNA中SATB1基因 5′上游序列的 - 2 95 5～ - 9片段 ,构建了 3个分别由SATB1基因 5′上游 - 2 95 5～ - 9,- 172 7～ - 9和 - 76 0～ - 9序列片段驱动的报告载体 -pGL3 SP2 94 6 luc ,pGL3 SP1718 luc和pGL3 SP75 1 luc ,分别瞬时转染JurkatT ,K5 6 2 ,U937和HeLa细胞 ,通过测定荧光素酶的表达活性 ,观察SATB1基因 5′上游序列片段 3个删除突变体在不同细胞内活性的差异 .结果显示 ,SATB1上游序列- 2 95 5 - 9在 4种细胞中的转录激活能力为U937>JurkatT >K5 6 2 ,在HeLa细胞中基本无激活 ,提示SATB1的转录激活可能具有一定的细胞类型特异性 .3种 5′删除突变体转录激活性由大至小顺序为 - 76 0 - 9>- 2 95 5 - 9>- 172 7 - 9,提示SATB1的核心启动子可能存在于其 5′上游序列的- 76 0至 - 9bp区域中 .     

水稻矮缩病毒小外壳蛋白基因的合成、克隆和序列分析

从感染水稻矮缩病毒(RDV)的水稻叶片中分离纯化了RDV,用人工合成的寡核苷酸为引物,合成了长度为1.0kb的小外壳蛋白基因,经PCR扩增后,克隆至pUC-19载体上。以双脱氧链终止法测序得到其全长序列,同已发表的RDV日本分离物小外壳蛋白基因序列相比有很高的同源率。     

Allele Polymorphism of a New Pentanucleotide STR Marker Located to an Intron of the Tumor Suppressor Gene ING1

Using polymerase chain reaction (PCR) DNA samples of unrelated subjects from the Volga-Ural region of Russia were examined to study allele polymorphism of the pentanucleotide repeat (TTGTG) _g localized to an intron of the tumor suppressor gene ING1. STR marker was registered in the EMBL database with the accession number AJ277387. In a sample of 119 individuals, three pentanucleotide alleles consisting of seven, eight, and nine repeated monomers were revealed. The allele frequencies were 0.24, 0.74, and 0.02, respectively. Heterozygosity was 0.45. On the basis of these data, the repeat can be regarded as a polymorphic STR marker for the ING1 gene and used in population and clinical studies.     

人SATB1基 5'上游序列的转录激活功能分析

在对人SATB1基因进行生物信息学分析的基础上,采用PCR技术,扩增人基因组DNA中SATB1基因5'上游序列的-2955～-9片段,构建了3个分别由SATB1基因5'上游-2955～-9,-1727～-9和-760～-9序列片段驱动的报告载体-pGL3-SP2946-luc,pGL3-SP1718-luc和pGL3-SP751-luc,分别瞬时转染Jurkat T,K562,U937和HeLa细胞,通过测定荧光素酶的表达活性,观察SATB1基因5'上游序列片段3个删除突变体在不同细胞内活性的差异.结果显示,SATB1上游序列-2955/-9在4种细胞中的转录激活能力为U937>Jurkat T>K562,在HeLa细胞中基本无激活,提示SATB1的转录激活可能具有一定的细胞类型特异性.3种5'删除突变体转录激活性由大至小顺序为-760/-9>-2955/-9>-1727/-9,提示SATB1的核心启动子可能存在于其5'上游序列的-760至-9 bp区域中.     

Molecular Evolution of the Small Subunit of Ribulose Bisphosphate Carboxylase: Nucleotide Substitution and Gene Conversion

The nucleotide sequences encoding the mature portion of 31 ribulose 1.5-bisphosphate carboxylase small subunit (SSU) genes from 17 genera of plants, green algae and cyanobacteria were examined. Among the 465 pairwise sequence comparisons, SSU multigene family members within the same species were more similar to each other in nonsynonymous or replacement nucleotide substitutions (RNS) than they were to SSU sequences in any other organism. The concerted evolution of independent SSU gene lineages within closely related plant species suggests that homogenization of RNS positions has occurred at least once in the life of each genus. The rate of expected RNS among mature SSU sequences was calculated to be 1.25 X 10(-9)/site/yr for the first 70 million years (MY) of divergence with a significant slowing to 0.13 X 10(-9)/site/yr for the next 1,400 MY. The data suggest that mature SSU sequences do not accumulate more than 20% differences in the RNS positions without compensatory changes in other components of this enzyme system. During the first 70 MY of divergence between species, the rate of expected synonymous or silent nucleotide substitutions (SNS) is approximately 6.6 X 10(-9)/site/yr. This is five times the RNS rate and is similar to the silent rate observed in animals. In striking contrast, SNS and RNS do not show this correlation among SSU gene family members within a species. A mechanism involving gene conversion within the exons followed by selection for biased gene conversion products with conservation of RNS positions and divergence of SNS positions is discussed. A SSU gene tree based on corrected RNS for 31 SSU sequences is presented and agrees well with a species tree based on morphological and cytogenetic traits for the 17 genera examined. SSU gene comparisons may be useful in predicting phylogenetic relationships and in some cases divergence times of various plant, algal and cyanobacterial species.     

Variation in the Pattern of Nucleotide Substitution Across Sites

A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the transition/transversion rate bias across sites provided a significant improvement in fit for most protein coding genes but not for the pseudogene. When the analysis was repeated with parameters estimated separately for first, second, and third codon positions, strong heterogeneity was uncovered for the first and second codon positions; the variation in the transition/transversion rate was generally weaker at the third codon position. The transition rate bias and branch lengths are underestimated when variation in the transition/transversion rate was not accommodated, suggesting that it may be important to accommodate variation in the pattern of nucleotide substitution for accurate estimation of evolutionary parameters. Received: 4 November 1997 / Accepted: 19 May 1998     

E-钙粘蛋白基因启动子区域单核苷酸基因多态性(-160A/C)和大肠癌遗传易感性的联系

目的:探讨E-钙粘蛋白基因(CDH1)启动子区域-160A/C单核苷酸基因多态性(single nucleotide polymorphism,SNP)和中国地区散发大肠癌(colorectal cancer,CRC)人群遗传易感性的联系。方法:以中国地区大肠癌病人群为研究基础,同时建立无肿瘤家族史以及其它遗传性疾病史的正常对照组,进行病例对照研究,采用聚合酶链反应-限制性片段长度多态性技术(polymerasechain reaction-restriction fragment length polymorphism,PCR-RFLP)行目的基因的多态性测定,同时行正常结肠组织和大肠癌组织的E-钙粘蛋白的免疫组化测定。结果:正常对照组和大肠癌组的目的基因型分布频率并无统计学差异(x2检验,P=0.602),同时A基因型和C基因型在正常结肠组织和大肠癌组织中E-钙粘蛋白的表达量也并无差异(t检验,P>0.05)。结论:CDH1启动子区域-160A/C单核苷酸基因多态性中并不单独增加大肠癌的发病风险。