Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution

Evaluation of Candidate Genes in the Absence of Positional Information: A Poor Bet on a Blind Dog!

More than 350 inherited diseases have been reported in dogs and at least 50% of them have human counterparts. To remove the diseases from dog breeds and to identify canine models for human diseases, it is necessary to find the mutations underlying them. To this end, two methods have been used: the functional candidate gene approach and linkage analysis. Here we present an evaluation of these in canine retinal diseases, which have been the subject of a large number of molecular genetic studies, and we show the contrasting outcomes of these approaches when dealing with genetically heterogeneous diseases. The candidate gene approach has led to 377 published results with 23 genes. Most of the results (66.6%) excluded the presence of a mutation in a gene or its coding region, while only 3.4% of the results identified the mutation causing the disease. On the other hand, five linkage analysis studies have been done on retinal diseases, resulting in three identified mutations and two mapped disease loci. Mapping studies have relied on dog research colonies. If this favorable application of linkage analysis can be extended to dogs in the pet population, success in identifying canine mutations could increase, with advantages to veterinary and human medicine.

Progress toward the production of long-chain polyunsaturated fatty acids in transgenic plants

Long-chain PUFA such as eicosapentaenoic and docosahexaenoic acids are prevalent in fish oils, and these compounds have been demonstrated to play important roles in human health and nutrition. In particular, these n-3/omega-3 long-chain PUFA provide protection from cardiovascular disease and a collection of symptoms (termed metabolic syndrome) associated with progression toward type 2 diabetes and obesity. Within Western populations, a large increase in the occurrence of these conditions represents a major public health concern. Unfortunately, both marine fish stocks and (consequentially) consumption of fish oils are in steep decline, limiting the protective role of long-chain PUFA in human health. One alternative approach to the provision of these health-beneficial FA is via their synthesis in transgenic plants. This review will describe recent advances in the production of transgenic plant oils nutritionally enhanced to produce long-chain PUFA.

Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding Loci

To develop new strategies for searching for genetic associations with complex human diseases, we analyzed 2784 single-nucleotide polymorphisms (SNPs) in 396 protein-coding genes involved in biological processes relevant to cancer and other complex diseases, with respect to gene diversity within samples of individuals representing the three major historic human populations (African, European, and Asian) and with respect to interpopulation genetic distance. Reduced levels of both intrapopulation gene diversity and interpopulation genetic distance were seen in the case of SNPs located within the 5'-UTR and at nonsynonymous SNPs, causing radical changes to protein structure. Reduction of gene diversity at SNP loci in these categories was evidence of purifying selection acting at these sites, which in turn causes a reduction in interpopulation divergence. By contrast, a small number of SNP sites in these categories revealed unusually high genetic distances between the two most diverged populations (African and Asian); these loci may have historically been subject to divergent selection pressures.

Functionally distinct polymorphic sequences in the human genome that are targets for p53 transactivation

The p53 tumor suppressor protein is a master regulatory transcription factor that coordinates cellular responses to DNA damage and cellular stress. Besides mutations in p53, or in proteins involved in the p53 response pathway, genetic variation in promoter response elements (REs) of p53 target genes is expected to alter biological responses to stress. To identify SNPs in p53 REs that may modify p53-controlled gene expression, we developed an approach that combines a custom bioinformatics search to identify candidate SNPs with functional yeast and mammalian cell assays to assess their effect on p53 transactivation. Among approximately 2 million human SNPs, we identified >200 that seem to disrupt functional p53 REs. Eight of these SNPs were evaluated in functional assays to determine both the activity of the putative RE and the impact of the candidate SNPs on transactivation. All eight candidate REs were functional, and in every case the SNP pair exhibited differential transactivation capacities. Additionally, six of the eight genes adjacent to these SNPs are induced by genotoxic stress or are activated directly by transfection with p53 cDNA. Thus, this strategy efficiently identifies SNPs that may differentially affect gene expression responses in the p53 regulatory pathway.

The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs

We analyzed the neighboring-nucleotide composition of 433,192 biallelic substitutions, representing the largest public collection of SNPs across the mouse genome. Large neighboring-nucleotide biases relative to the genome- or chromosome-specific average were observed at the immediate adjacent sites and small biases extended farther from the substitution site. For all substitutions, the biases for A, C, G, and T were 0.21, 2.63, 0.71, and -3.55%, respectively, on the immediate adjacent 5' site and -3.67, 0.75, 2.69, and 0.23%, respectively, on the immediate adjacent 3' side. Further examination of the six categories of substitution revealed that the neighboring-nucleotide patterns for transitions were strongly influenced by the hypermutability of dinucleotide CpG and the neighboring effects on transversions were complex. Probability of a transversion increased with increasing A + T content of the two immediate adjacent sites, which was similarly observed in the human and Arabidopsis genomes. Overall, the bias patterns for the neighboring nucleotides in the mouse and human genomes were essentially the same; however, the extent of the biases was notably less in mice. Our results provide the first comprehensive view of the neighboring-nucleotide effects in the mouse genome and are important for understanding the mutational mechanisms and sequence evolution in the mammalian genomes.

Bacterial artificial chromosome-derived molecular markers for early bolting in sugar beet

Early bolting in sugar beet (Beta vulgaris L.) is controlled by the dominant gene B. From an incomplete physical map around the B gene, 18 bacterial artificial chromosomes (BACs) were selected for marker development. Three BACs were shotgun-sequenced, and 61 open reading frames (ORFs) were identified. Together with 104 BAC ends from 54 BACs, a total number of 55,464 nucleotides were sequenced. Of these, 37 BAC ends and 12 ORFs were selected for marker development. Thirty-one percent of the sequences were found to be single copy and 24%, low copy. From these sequences, 15 markers from ten different BACs were developed. Ten polymorphisms were determined by simple agarose gel electrophoresis of either restricted or non-restricted PCR products. Another five markers were determined by tetra-primer amplification refractory mutation system-PCR. In order to select candidate BACs for cloning the gene, genetic linkage between seven markers and the bolting gene was calculated using 1,617 plants from an F2 population segregating for early bolting. The recombination values ranged between 0.0033 and 0.0201. In addition, a set of 41 wild and cultivated Beta accessions differing in their early bolting character was genotyped with seven markers. A common haplotype encompassing two marker loci and the b allele was found in all sugar beet varieties, indicating complete linkage disequilibrium between these loci. This suggests that the bolting gene is located in close vicinity to these markers, and the corresponding BACs can be used for cloning the gene.

Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells

Human embryonic stem (ES) cells are pluripotent cells derived from blastocyst-stage embryos. It has been suggested that these cells should play a major role in transplantation medicine and be able to advance our knowledge in human embryology. We propose that these cells should also play a vital role in the creation of models of human disorders. This aspect would be most valuable where animal models failed to faithfully recapitulate the human phenotype. Lesch-Nyhan disease is caused by a mutation in the HPRT1 gene that triggers an overproduction of uric acid, causing gout-like symptoms and urinary stones, in addition to neurological disorders. Due to biochemical differences between humans and rodents, a mouse lacking the HPRT expression will fail to accumulate uric acid. In this research we demonstrate a model for Lesch-Nyhan disease by mutating the HPRT1 gene in human ES cells using homologous recombination. We have verified the mutation in the HPRT1 allele at the DNA and RNA levels. By using selection media, we show that HPRT1 activity is abolished in the mutant cells, and the HPRT1-cells show a higher rate of uric acid accumulation than the wild-type cells. Therefore, these cells recapitulate to some extent the characteristics of Lesch-Nyhan syndrome and can help researchers further investigate this genetic disease and analyze drugs that will prevent the onset of its symptoms. We therefore suggest that human diseases may be modeled using human ES cells.

Specific recognition of napthyridine-based ligands toward guanine-containing bulges in RNA duplexes and RNA–DNA heteroduplexes

Mismatched bulges in nucleic acid constructs are important in the recognition event between biological molecules. Herein, it is observed that napthyridine dimer 2 is able to specifically bind G-G mismatches in all nucleic acid constructs comprising of RNA-RNA, RNA-DNA and DNA-DNA duplexes. However, the binding affinity of 2 is strongest toward DNA duplex, followed by RNA-DNA heteroduplex and RNA duplex being the weakest binding partner. Nonetheless, this binding behavior suggests that the binding process primarily occurs between the guanine base pairs and the napthyridine moiety, and is independent of the tertiary structure of the nucleic acid duplexes.

Evidence for abundant slightly deleterious polymorphisms in bacterial populations

The nearly neutral theory of molecular evolution predicts that slightly deleterious mutations subject to purifying selection are widespread in natural populations, particularly those of large effective population size. To test this hypothesis, the standardized difference between pairwise nucleotide difference and number of segregation sites (corrected for number of sequences) was estimated for 149 population data sets from 84 species of bacteria. This quantity (Tajima's D-statistic) was estimated separately for synonymous (D(syn)) and nonsynonymous (D(non)) polymorphisms. D(syn) was positive in 70% of data sets, and the overall median D(syn) (0.873) was positive. By contrast D(non) was negative in 68% of data sets, and the overall median D(non) (-0.656) was negative. The preponderance of negative values of D(non) is evidence that there are widespread rare nonsynonymous polymorphisms in the process of being eliminated by purifying selection, as predicted to occur in populations with large effective size by the nearly neutral theory. The major exceptions to this trend were seen among surface proteins, particularly those of bacteria parasitic on vertebrates, which included a number of cases of polymorphisms apparently maintained by balancing selection.

Single-nucleotide polymorphisms in genes relating to homocysteine metabolism: how applicable are public SNP databases to a typical European population?

To facilitate the association studies in complex diseases characterized by hyperhomocysteinemia, we collected structural and frequency data on single-nucleotide polymorphism (SNPs) in 24 genes relating to homocysteine metabolism. Firstly, we scanned approximately 1.2 Mbp of sequence in the NCBI SNP database (dbSNP) build 110 and we detected 1353 putative SNPs with an average in silico genic density of 1:683. Out of 112 putative SNPs in coding regions (cSNPs), we selected a subset of 42 cSNPs and we assessed the applicability of the NCBI dbSNP to the Czech population - a typical representative of European Caucasians - by determining the frequency of the putative cSNPs experimentally by PCR-RFLP or ARMS-PCR in at least 110 control Czech chromosomes. As only 25 of the 42 analyzed cSNPs met the criterion of >/=1% frequency, the positive predictive value of the NCBI data set for our population reached 60%, which is similar to other studies. The correlation of SNP frequency between Czechs and other Caucasians - obtained from NCBI and/or literature - was stronger (r(2)=0.90 for 20 cSNPs) than between Czechs and general NCBI database entries (r(2)=0.73 for 27 cSNPs). Moreover, frequencies of all 20 putative cSNPs, for which data in Caucasians were available, were congruently below or above the 1% frequency criterion both in Czechs and in other Caucasians. In summary, our study shows that the NCBI dbSNP is a useful tool for selecting cSNPs for genetic studies of hyperhomocysteinemia in European populations, although experimental validation of SNPs should be performed, especially if the cSNP entry lacks any frequency data in Caucasians.

Quantification in Proteomics through Stable Isotope Coding: A Review

This review focuses on techniques for quantification and identification in proteomics by stable isotope coding. Methods are examined for analyzing expression, post-translational modifications, protein:protein interactions, single amino acid polymorphism, and absolute quantification. The bulk of the quantification literature in proteomics focuses on expression analysis, where a wide variety of methods targeting different features of proteins are described. Methods for the analysis of post-translational modification (PTM) focus primarily on phosphorylation and glycosylation, where quantification is achieved in two ways, either by substitution or tagging of the PTM with an isotopically coded derivatizing agent in a single process or by coding and selecting PTM modified peptides in separate operations. Absolute quantification has been achieved by age-old internal standard methods, in which an isotopically labeled isoform of an analyte is synthesized and added to a mixture at a known concentration. One of the surprises is that isotope coding can be a valuable aid in the examination of intermolecular association of proteins through stimulus:response studies. Preliminary efforts to recognize single amino acid polymorphism are also described. The review ends with the conclusion that (1) isotope ratio analysis of protein concentration between samples does not necessarily relate directly to protein expression and rate of PTM and (2) that multiple new methods must be developed and applied simultaneously to make existing stable isotope quantification methods more meaningful. Although stable isotope coding is a powerful, wonderful new technique, multiple analytical issues must be solved for the technique to reach its full potential as a tool to study biological systems.

Genómica de la regulación del peso corporal: mecanismos moleculares que predisponen a la obesidad

Obesity has become a worldwide public health problem which affects millions of people. Substantial progress has been made in elucidating the pathogenesis of energy homeostasis over the past few years. The fact that obesity is under strong genetic control has been well established. Twin, adoption and family studies have shown that genetic factors play a significant role in the pathogenesis of obesity. Human monogenic obesity is rare in large populations. The most common form of obesity is considered to be a polygenic disorder. New treatments are currently required for this common metabolic disease and type 2 diabetes. The identification of physiological and biochemical factors that underlie the metabolic disturbances observed in obesity is a key step in developing better therapeutic outcomes. The discovery of new genes and pathways involved in the pathogenesis of such a disease is critical to this process. However, identification of genes that contribute to the risk of developing the disease represents a significant challenge since obesity is a complex disease with many genetic and environmental causes. A number of diverse approaches have been used to discover and validate potential new genes for obesity. To date, DNA-based approaches using candidate genes and genome-wide linkage analysis have not had a great success in identifying genomic regions or genes involved in the development of these diseases. Recent advances in the ability to evaluate linkage analysis data from large family pedigrees (using variance components-based linkage analysis) show great promise in robustly identifying genomic regions associated with the development of obesity. Studying rare mutations in humans and animal models has provided fundamental insight into a complex physiological process, and has complemented population-based studies that seek to reveal primary causes. Remarkable progress has been made in both fronts and the pace of advance is likely to accelerate as functional genomics and the human genome project expand and mature. Approaches based on Mendelian and quantitative genetics may well converge, and ultimately lead to more rational and selective therapies.

Hierarchical analysis of 30 Y-chromosome SNPs in European populations

Analysis of Y-chromosome haplogroups defined by binary polymorphisms, has became a standard approach for studying the origin of modern human populations and for measuring the variability between them. Furthermore, the simplicity and population specificity of binary polymorphisms allows inferences to be drawn about the population origin of any male sample of interest for forensic purposes. From the 245 binary polymorphisms that can be analysed by PCR described in the Y Chromosome Consortium tree, we have selected 30 markers. The set of 30 has been grouped into 4 multiplexes in order to determine the most frequent haplogroups in Europe, using only 1 or 2 multiplexes. In this way, we avoid typing unnecessary SNPs to define the final haplogroup saving effort and cost, since we only need to type 9 SNPs in the best case and in the worst case, no more than 17 SNPs to define the haplogroup. The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit. A total of 292 samples from 8 different districts of Galicia (northwest Spain) were analysed with this strategy. No significant differences were detected among the different districts, except for the population from Marina Lucense, which showed a distant haplogroup frequency but not higher Phi(st) values.

Widespread purifying selection at polymorphic sites in human protein-coding loci

Estimation of gene diversity (heterozygosity) at 1442 single-nucleotide polymorphism (SNP) loci in an ethnically diverse sample of humans revealed consistently reduced gene diversities at SNP loci causing amino acid changes, particularly those causing amino acid changes predicted to be disruptive to protein structure. The reduction of gene diversity at these SNP loci, in comparison to SNPs in the same genes not affecting protein structure, is evidence that negative natural selection (purifying selection) has reduced the population frequencies of deleterious SNP alleles. This, in turn, suggests that slightly deleterious mutations are widespread in the human population and that estimation of gene diversity even in a sample of modest size can help guide the search for disease-associated genes.