人类基因组SNPs的研究现状及应用前景

基因组DNA是生物体各种生理、病理性状的物质基础,人类DNA序列变异约90%表现为单核苷酸多态性(singlenucleotidepolymorphisms,SNPs),这是一种常见的遗传变异类型,在人类基因组中广泛存在,被认为是人类疾病易感性和药物反应的决定性因素。本文主要介绍了SNPs的分类及特点、人类基因组SNPs的研究现状、SNPs在实践中的应用,以及SNPs在遗传作图、医药、遗传易感性、个体化医疗等方面的研究前景,并探讨了当前SNPs研究中存在的问题。     

Uniformity of organellar DNA in Aldrovanda vesiculosa, an endangered aquatic carnivorous species, distributed across four continents

Organellar DNA from the widely distributed but rare and critically endangered aquatic carnivorous plant Aldrovanda vesiculosa (Droseraceae) was examined. Six chloroplast intergenic regions (3700 nt in total) were sequenced before analyzing the Southern-RFLP (Restriction Fragment Length Polymorphism) of 2 mt gene flanking regions. Only two different chloroplast haplotypes among 15 A. vesiculosa accessions from Africa, Australia, Europe, and Japan were found, generally distinguishing European and non-European plants, with two exceptions. Genetic variation observed in A. vesiculosa appears to be even lower than in other aquatic species with a similar world-wide distribution. A recent bottleneck followed by long-distance dispersal by water birds or low mutation rates could be responsible for the observed genetic uniformity. Estimation of genetic distances based on six chloroplast intergenic regions led to the conclusion that the chloroplast genome of A. vesiculosa matches more closely to that of Drosera regia than Dionaea muscipula, a sister genus sharing snapping traps. The inconsistency between genetic distance estimates based on nuclear and cytoplasmic markers may reflect a chloroplast capture. In A. vesiculosa, a four amino acids substitution (TGWS) in the amino acid sequence of ATP synthase alpha subunit (ATP1), highly conserved mitochondrial protein, was discovered, unique among all organisms based on current knowledge.     

Chloroplast sequences reveal a diversity gradient in the Mediterranean Ruppia cirrhosa species complex

Two subcosmopolitan species Ruppia maritima and Ruppia cirrhosa are recognized throughout Europe, whereas Ruppia drepanensis is endemic to SW Europe. We aimed at characterizing the geographic structure of the chloroplast DNA haplotype diversity of 56 Ruppia populations across the European part of the Mediterranean. On the basis of five cpDNA markers (total length of 2300 bp) 16 haplotypes were obtained for 1546 individuals. Three populations of R. maritima showed a single haplotype and differed in five insertions/deletions and 16 substitutions from a highly variable R. cirrhosa species complex, which included R. drepanensis. The haplotype diversity of this species complex was much higher in the western Mediterranean basin than in the eastern basin. Analysis of molecular variance (AMOVA) showed significant differentiation of R. cirrhosa between the two basins and also within the western Mediterranean thereby suggesting the latter as an important centre of Ruppia diversity. An isolation-by-distance (IBD) pattern was stronger between the West-East basin populations than within basins. A PCO analysis of the western basin populations indicated a diversity gradient with those of Sardinia as polymorph intermediates. The low diversity within the eastern basin suggests that the observed gradient could be hypothesized as a historical dispersal of only a limited number of haplotypes from west to east.     

Promoter hypomethylation contributes to the expression of MUC3A in cancer cells

MUC3A is a membrane-bound glycoprotein that is aberrantly expressed in carcinomas and is a risk factor for a poor prognosis. However, the exact mechanism of MUC3A expression has yet to be clarified. Here, we provide the first evidence that MUC3A gene expression is controlled by the CpG methylation status of the proximal promoter region. We show that the DNA methylation pattern is intimately correlated with MUC3A expression in breast, lung, pancreas and colon cancer cell lines. The DNA methylation status of 30 CpG sites from −660 to +273 was mapped using MassARRAY analysis. MUC3A-negative cancer cell lines and those with low MUC3A expression (e.g., MCF-7) were highly methylated in the proximal promoter region, corresponding to 9 CpG sites (−345 to −75 bp), whereas MUC3A-positive cell lines (e.g., LS174T) had low methylation levels. Moreover, 5-aza-2′-deoxycytidine and trichostatin A treatment of MUC3A-negative cells or those with low MUC3A expression caused elevation of MUC3A mRNA. Our results suggest that DNA hypomethylation in the 5′-flanking region of the MUC3A gene plays an important role in MUC3A expression in carcinomas of various organs. An understanding of epigenetic changes in MUC3A may contribute to the diagnosis of carcinogenic risk and to prediction of outcome in patients with cancer.     

Purkinje cells originate from cerebellar ventricular zone progenitors positive for Neph3 and E-cadherin

GABAergic Purkinje cells (PCs) provide the primary output from the cerebellar cortex, which controls movement and posture. Although the mechanisms of PC differentiation have been well studied, the precise origin and initial specification mechanism of PCs remain to be clarified. Here, we identified a cerebellar and spinal cord GABAergic progenitor-selective cell surface marker, Neph3, which is a direct downstream target gene of Ptf1a, an essential regulator of GABAergic neuron development. Using FACS, Neph3⁺ GABAergic progenitors were sorted from the embryonic cerebellum, and the cell fate of this population was mapped by culturing in vitro. We found that most of the Neph3⁺ populations sorted from the mouse E12.5 cerebellum were fated to differentiate into PCs while the remaining small fraction of Neph3⁺ cells were progenitors for Pax2⁺ interneurons, which are likely to be deep cerebellar nuclei GABAergic neurons. These results were confirmed by short-term in vivo lineage-tracing experiments using transgenic mice expressing Neph3 promoter-driven GFP. In addition, we identified E-cadherin as a marker selectively expressed by a dorsally localized subset of cerebellar Neph3⁺ cells. Sorting experiments revealed that the Neph3⁺ E-cadherin^high population in the embryonic cerebellum defined PC progenitors while progenitors for Pax2⁺ interneurons were enriched in the Neph3⁺ E-cadherin^low population. Taken together, our results identify two spatially demarcated subregions that generate distinct cerebellar GABAergic subtypes and reveal the origin of PCs in the ventricular zone of the cerebellar primordium.     

BRCA1 negatively regulates formation of autophagic vacuoles in MCF-7 breast cancer cells

In recent years, the function of different tumour suppressors in the regulation of macroautophagy has been studied. We show here that BRCA1, unlike other tumour suppressors, negatively regulates formation of autophagosomes and lysosomal mass under conditions of both basal and enhanced autophagy. In MCF-7 breast cancer cells, increased formation of autophagic vacuoles after inactivation of BRCA1 by siRNAs is associated with an increase in reactive oxygen species, such as superoxide anion and hydrogen peroxide. This allows one to propose an antioxidant function for BRCA1 and suggests that dysfunctional mitochondria and the generated reactive oxygen species excess could explain the increased macroautophagy observed in the absence of BRCA1. In addition, a quick decrease in BRCA1 levels occurs when MCF-7 cells are switched to a nutrient-poor environment that stimulates macroautophagy and that is also reminiscent of certain phases of tumour growth. Inhibition of BRCA1 synthesis has an important role in this reduction, while there are almost no changes in BRCA1 degradation by lysosomes and proteasomes. Therefore, BRCA1 produces macroautophagy inhibition by reducing the formation of autophagic vacuoles, and this, together with the other results presented here, shows new functional aspects of BRCA1 that could help to clarify the role of autophagy in cancer development.     

Structural Bases for Stability-Function Tradeoffs in Antibiotic Resistance

Preorganization of enzyme active sites for substrate recognition typically comes at a cost to the stability of the folded form of the protein; consequently, enzymes can be dramatically stabilized by substitutions that attenuate the size and preorganization “strain” of the active site. How this stability-activity tradeoff constrains enzyme evolution has remained less certain, and it is unclear whether one should expect major stability insults as enzymes mutate towards new activities or how these new activities manifest structurally. These questions are both germane and easy to study in β-lactamases, which are evolving on the timescale of years to confer resistance to an ever-broader spectrum of β-lactam antibiotics. To explore whether stability is a substantial constraint on this antibiotic resistance evolution, we investigated extended-spectrum mutants of class C β-lactamases, which had evolved new activity versus third-generation cephalosporins. Five mutant enzymes had between 100-fold and 200-fold increased activity against the antibiotic cefotaxime in enzyme assays, and the mutant enzymes all lost thermodynamic stability (from 1.7 kcal mol^− 1 to 4.1 kcal mol^− 1), consistent with the stability-function hypothesis. Intriguingly, several of the substitutions were 10-20 Å from the catalytic serine; the question of how they conferred extended-spectrum activity arose. Eight structures, including complexes with inhibitors and extended-spectrum antibiotics, were determined by X-ray crystallography. Distinct mechanisms of action, including changes in the flexibility and ground-state structures of the enzyme, are revealed for each mutant. These results explain the structural bases for the antibiotic resistance conferred by these substitutions and their corresponding decrease in protein stability, which will constrain the evolution of new antibiotic resistance.     

Fluctuations in the incubation moisture environment affect growth but not survival of hatchling lizards

Few studies have collected longitudinal data that follow the complete microevolutionary path of an organism linking sources of variation (e.g. environmental versus genetic) to a trait and its subsequent relationship with fitness. Identifying the links within this pathway is imperative for understanding the ecological relevance of effects found at the phenotypic level. Furthermore, experimental studies that examine parts of the pathway in ectothermic organisms often fail to mimic the complexities of the natural developmental environment. Temperature and moisture conditions in reptile nests, for example, can fluctuate greatly on a seasonal and daily basis. Despite the potential effects of fluctuating environments, the vast majority of studies have held environmental treatments constant during the developmental period. We investigated the effects of fluctuating moisture regimes during incubation on eggs, hatchling phenotypes, and subsequent survival in the eastern fence lizard Sceloporus undulatus. Moisture fluctuations during embryonic development caused water absorption by eggs to follow the environmental availability of moisture. Initial hatchling tail length was affected by the pattern of moisture fluctuations, and hatchling growth rates in fluctuating treatments were significantly faster than those in a constant treatment, resulting in larger hatchlings after 4 weeks. A release–recapture experiment conducted in the field did not detect a treatment effect on survival despite the larger body sizes. In summary, although fluctuations affected water absorption by eggs and some hatchling traits, these effects did not have subsequent fitness consequences. The results obtained suggest that egg and hatchling survival are buffered against natural soil moisture fluctuations during incubation, even when egg and hatchling traits are significantly affected. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 89–102.     

利用SRAP标记分析中国野生石蒜的遗传多样性

采用SRAP（Sequence-related amplified polymorphism,序列相关扩增多态性）标记对中国13个省24份野生石蒜（Lycoris radiata）资源94个样品进行了检测。10个引物组合共扩增出218条带,其中173条为多态性条带,多态性百分比达79.36%。石蒜的观测等位基因数（na）、有效等位基因数（ne）、基因多样性指数（h）、Shannon信息指数（I）分别为1.7936、1.4131、0.2415和0.3664。石蒜不同种源间的遗传分化系数（Gst）达0.9547、基因流（Nm）仅0.0136,表明种源间遗传分化显著,遗传变异主要存在于种源间。根据Nei′s遗传距离对24份种源进行UPGMA聚类,所有石蒜种源聚成两大类,第I大类由7份种源组成,除江苏连云港的石蒜（JS3）外,均来自我国西南或西北地区;其余的17份种源构成第II大类,它们遍及华南、华中和华东地区;各大类中的分支结果与野生石蒜外部形态及生长发育习性有一定联系。将石蒜种源的遗传多样性与其所处的经度、纬度、海拔、年均降雨量、年均温等进行相关性分析,结果显示它们之间的相关性均不显著,即石蒜对环境依赖性小,能分布在各种生境中。根据以上结果,我们认为野生石蒜具有较丰富的遗传多样性,而种源间遗传分化显著的原因主要是基因流的隔离。研究结果对我国的野生石蒜资源的开发利用与保护有重要意义。     

Phenylethanoid glycosides from Lippia javanica

Lippia javanica (N.L.Burm.) Spreng. is an aromatic, multipurpose medicinal plant from which a number of volatile compounds have been identified, together with toxic triterpenoids and iridoid glycosides. Two additional phenylethanoid glycosides, verbascoside and isoverbascoside, were isolated from L. javanica and characterized. High performance liquid chromatography analyses of polar extracts of three other Lippia species (L. scaberrima, L. rehmannii and L. wilmsii), indigenous to South Africa, revealed the presence of both isomers. When compared to the other indigenous Lippia species, the leaves of L. javanica were found to contain the highest concentrations of both isomers. In addition, the intraspecies variation of the verbascoside/isoverbascoside content of L. javanica, harvested from the same and different localities, was investigated. The concentrations of the two phenylethanoids remained fairly consistent within and between different populations, even when geographically separated. While these compounds are produced by many genera, they may now be added to the list of iridoid glucosides employed as chemotaxonomic markers for Lippia species.