The evolution of gene expression QTL in Saccharomyces cerevisiae

Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

Gene-expression variation within and among human populations

Understanding patterns of gene-expression variation within and among human populations will provide important insights into the molecular basis of phenotypic diversity and the interpretation of patterns of expression variation in disease. However, little is known about how gene-expression variation is apportioned within and among human populations. Here, we characterize patterns of natural gene-expression variation in 16 individuals of European and African ancestry. We find extensive variation in gene-expression levels and estimate that approximately 83% of genes are differentially expressed among individuals and that approximately 17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Finally, we performed allele-specific quantitative polymerase chain reaction to demonstrate that cis-regulatory variation in the lymphocyte adaptor protein (SH2B adapter protein 3) contributes to differential expression between European and African samples. These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci.

Genomewide evolutionary rates in laboratory and wild yeast

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

Local regulatory variation in Saccharomyces cerevisiae

Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such regulatory variation can occur both at the same locus as the gene whose expression it affects (local regulatory variation) and elsewhere in the genome at trans-acting factors. Here we present a detailed analysis of genome-wide local regulatory variation in Saccharomyces cerevisiae. We used genetic linkage analysis to show that nearly a quarter of all yeast genes contain local regulatory variation between two divergent strains. We measured allele-specific expression in a diploid hybrid of the two strains for 77 genes showing strong self-linkage and found that in 52%–78% of these genes, local regulatory variation acts directly in cis. We also experimentally confirmed one example in which local regulatory variation in the gene AMN1 acts in trans through a feedback loop. Genome-wide sequence analysis revealed that genes subject to local regulatory variation show increased polymorphism in the promoter regions, and that some but not all of this increase is due to polymorphisms in predicted transcription factor binding sites. Increased polymorphism was also found in the 3′ untranslated regions of these genes. These findings point to the importance of cis-acting variation, but also suggest that there is a diverse set of mechanisms through which local variation can affect gene expression levels.

Variation in DNA sequences in and around a gene can contribute to differences between individuals by affecting the gene's expression. The authors have used a variety of methods to characterize this local DNA sequence variation on a large scale in two strains of the budding yeast Saccharomyces cerevisiae. Their results suggest that the expression levels of a sizeable fraction of genes are affected by local sequence variation. Many local variants alter the expression of only one of two copies of a gene in diploid hybrid yeast, but other local variants can affect both copies equally. The authors also found that sequence variation in particular regions of DNA near genes, both upstream and downstream of coding sequences and especially in transcription factor binding sites, is most likely to affect gene expression. These results provide a detailed view of local sequence variation that affects the expression of nearby genes in S. cerevisiae.

Genome-wide scans for loci under selection in humans

Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection.

Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays

Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to perform genotyping on genomic DNA. Here, we show that in segregants from a cross between two unrelated strains of Saccharomyces cerevisiae, high-quality genotype data can also be obtained when mRNA is hybridized to an oligonucleotide-expression array. We were able to identify and genotype nearly 1000 polymorphisms at an error rate close to 3% in segregants and at an error rate of 7% in diploid strains, a performance comparable to methods using genomic DNA. In addition, we demonstrate how simultaneous genotyping and gene-expression profiling can reveal cis-regulatory variation by screening hundreds of genes for allele-specific expression. With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two S. cerevisiae strains.

Elevated amyloid β protein (Aβ42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene

Plasma amyloid beta protein (Abeta42) levels and late onset Alzheimer's disease (LOAD) have been linked to the same region on chromosome 10q. The PLAU gene within this region encodes urokinase-type plasminogen activator, which converts plasminogen to plasmin. Abeta aggregates induce PLAU expression thereby increasing plasmin, which degrades both aggregated and non-aggregated forms of Abeta. We evaluated single nucleotide polymorphisms (SNPs) in PLAU for association with Abeta42 and LOAD. PLAU SNP compound genotypes composed of haplotype pairs showed significant association with AD in three independent case-control series. PLAU SNP haplotypes associated significantly with plasma Abeta42 in 10 extended LOAD families. One of the SNPs analyzed was a missense C/T polymorphism in exon 6 of PLAU (PLAU_1=rs2227564), which causes a proline to leucine change (P141L). We analyzed PLAU_1 for association with AD in six case-control series and 24 extended LOAD families. The CT and TT PLAU_1 genotypes showed association (P=0.05) with an overall estimated odds ratio of 1.2 (1.0-1.5). The CT and TT genotypes of PLAU_1 were also associated with significant age-dependent elevation of plasma Abeta42 in 24 extended LOAD families (P=0.0006). In knockout mice lacking the PLAU gene, plasma--but not brain--Abeta42 as well as Abeta40 was significantly elevated, also in an age-dependent manner. The PLAU_1 associations were independent of the associations we found among plasma Abeta42, LOAD and variants in the IDE or VR22 region. These results provide strong evidence that PLAU or a nearby gene is involved in the development of LOAD. PLAU_1 is a plausible pathogenic mutation that could act by increasing Abeta42, but additional biological experiments are required to show this definitively.

Fine mapping of the alpha-T catenin gene to a quantitative trait locus on chromosome 10 in late-onset Alzheimer's disease pedigrees

Using plasma amyloid beta protein (Abeta42) levels as an intermediate, quantitative phenotype for late onset Alzheimer's disease (LOAD), we previously obtained significant linkage at approximately 80 cM on chromosome 10. Linkage to the same region was obtained independently in a study of affected LOAD sib-pairs. Together, these two studies provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta42. VR22 is a large (1.7 Mb) gene located at 80 cM that encodes alpha-T catenin, which is a binding partner of beta catenin. This makes VR22 an attractive candidate gene because beta catenin interacts with presenilin 1, which has many mutations that elevate Abeta42 and cause early onset familial AD. We identified two intronic VR22 SNPs (4360 and 4783) in strong linkage disequilibrium (LD) that showed highly significant association (P=0.0001 and 0.0006) with plasma Abeta42 in 10 extended LOAD families. This association clearly contributed to the linkage at approximately 80 cM because the lod scores decreased when linkage analysis was performed conditional upon the VR22 association. This association replicated in another independent set of 12 LOAD families (P=0.04 for 4783 and P=0.08 for 4360). Bounding of the association region using multiple SNPs showed VR22 to be the only confirmed gene within the region of association. These findings indicate that VR22 has variant(s) which influence Abeta42 and contribute to the previously reported linkage for plasma Abeta42 in LOAD families.

Obstructive sleep apnea patients use more health care resources ten years prior to diagnosis

Because Obstructive Sleep Apnea Syndrome (OSAS) patients may be treated for comorbidities prior to OSAS diagnosis, we examined the health care utilization records of 181 OSAS patients and those of matched controls. We compared OSA patient health care utilization for a ten-year interval prior to diagnosis to those of randomized age-, gender-, and geographically-matched controls from the general population. We found that OSAS patients used approximately twice the resources (as defined by physician claims and stays in hospital) in the ten years prior to their diagnosis. Physician claims for cases totaled $686,365 ($3,972 per patient) compared to $356,376 ($1,969 per patient) for the controls for the length of the study. Utilization was significantly higher in 7 of 10 years prior to diagnosis. OSAS patients also had more hospitalizations: they had 1,118 nights (6.2 per patient) in hospital versus 676 nights (3.7 per patient) for controls over the ten-year period. Thus OSA patients are heavy users of health care resources ten years prior to diagnosis.

Linkage of plasma Abeta42 to a quantitative locus on chromosome 10 in late-onset Alzheimer's disease pedigrees

Plasma Abeta42 (amyloid beta42 peptide) is invariably elevated in early-onset familial Alzheimer's disease (AD), and it is also increased in the first-degree relatives of patients with typical late-onset AD (LOAD). To detect LOAD loci that increase Abeta42, we used plasma Abeta42 as a surrogate trait and performed linkage analysis on extended AD pedigrees identified through a LOAD patient with extremely high plasma Abeta. Here, we report linkage to chromosome 10 with a maximal lod score of 3.93 at 81 centimorgans close to D10S1225. Remarkably, linkage to the same region was obtained independently in a genome-wide screen of LOAD sibling pairs. These results provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta.

Health care utilization in males with obstructive sleep apnea syndrome two years after diagnosis and treatment

OBJECTIVE

To document changes in health care utilization (physician claims and hospitalizations) two years after diagnosis and treatment of patients with OSAS.

DESIGN

Prospective observational cohort study.

SETTING

The study was done in the Canadian Province of Manitoba. OSAS patients were selected from a University-based sleep disorders center. Control subjects were selected from the general population.

PATIENTS AND CONTROLS

There were 344 OSAS patients on whom there was utilization data for the period of the study. They were matched to controls from the general population by gender, age, and geographic location.

MEASUREMENTS AND RESULTS

The difference in physician claims between the patients and their matched controls two years after diagnosis and treatment ($174+/-32.4 (SE) per year in Canadian dollars) was significantly less than the difference in the year before diagnosis ($260+/-35.7 (SE), p=0.038). Examining the subgroups of patients adhering (PAT) or not adhering (PNAT) to treatment revealed that the changes were only significant in the patients adhering to treatment. Hospital stays for the entire OSAS group decreased from 1.27 days+0.25(SE) per patient per year one year before diagnosis to 0.54+0.13 per patient per year (p=0.01). The changes in the PAT group (1.25+0.28 per patient per year one year before diagnosis to 0.53+0.14 per patient per year (p=0.034) were significant while in the PNAT group they were not.

CONCLUSIONS

Adherence to treatment in patients with OSAS results in a significant reduction in physician claims and hospital stays.

Health care utilization in the 10 years prior to diagnosis in obstructive sleep apnea syndrome patients

Obstructive sleep apnea syndrome (OSAS) patients may have symptoms for years prior to recognition of their disorder, or they may be treated for the associated comorbidities. We hypothesized that such patients would be heavy consumers of health care resources for several years prior to diagnosis. We therefore compared health service utilization for a 10-year interval prior to diagnosis of 181 OSA patients to those of randomly selected age-, gender-, and geographically matched controls from the general population. OSAS patients used approximately twice as many health care services (as defined by physician claims and overnight stays in hospital) in the 10 years prior to their initial diagnostic evaluation for apnea. Physician claims for the OSA patients totaled $686,365 ($3972 per patient), compared to $356,376 ($1969 per patient) for the controls for the 10-year period examined in this study. Use of health services was significantly higher in 7 of 10 years prior to diagnosis. The OSAS patients also had more overnight hospitalizations: they spent 1118 nights (6.2 per patient) in hospital vs 676 nights (3.7 per patient) for controls in the decade prior to diagnosis. We conclude that by the time patients are finally diagnosed for sleep apnea, they have already been heavy users of health services for several years. It is possible that our findings reflect not OSAS per se, but the presence of some of the risk factors that predispose to OSAS, such as obesity, alcohol usage and perhaps tobacco consumption.

Myoelectric prostheses for below-elbow amputees: the Trent experience

Experience of myoelectric prostheses for unilateral below-elbow amputees in a large region of Great Britain is presented. Of the cases considered, 14 were adults and 29 were 16 years of age or less. The rejection rate was 25% overall but it was lower in adults, at 17%. Comparisons with published data and other aspects of myoelectric prostheses are discussed. Just over half the 37 amputees interviewed were independent in activities of daily living; independence was more common in the adults, at 77%. A very large proportion of myoelectric prosthesis users also used body-powered prostheses, demonstrating a need for both types of prosthesis for optimum rehabilitation. It is recommended that myoelectric prosthetic programmes should be carried out from specialized centres with comprehensive facilities for this expensive rehabilitation aid.

Lead poisoning in rural Scotland

Nine people from four families living in rural parts of Scotland have been found to suffer from clinical or biochemical effects of lead poisoning. Five had symptoms and four had unequivocal evidence of excessive lead exposure. The source of lead has been traced to the domestic water supply which in all cases was grossly contaminated with lead acquired from lead plumbing systems, including lead storage tanks. Clinical improvement followed the replacement of lead piping in two families studied. Lead poisoning is a possible cause of chronic ill health in areas of plumbosolvent water.