Emerging patterns of epigenomic variation

Fuelled by new sequencing technologies, epigenome mapping projects are revealing epigenomic variation at all levels of biological complexity, from species to cells. Comparisons of methylation profiles among species reveal evolutionary conservation of gene body methylation patterns, pointing to the fundamental role of epigenomes in gene regulation. At the human population level, epigenomic changes provide footprints of the effects of genomic variants within the vast nonprotein-coding fraction of the genome, and comparisons of the epigenomes of parents and their offspring point to quantitative epigenomic parent-of-origin effects confounding classical Mendelian genetics. At the organismal level, comparisons of epigenomes from diverse cell types provide insights into cellular differentiation. Finally, comparisons of epigenomes from monozygotic twins help dissect genetic and environmental influences on human phenotypes and longitudinal comparisons reveal aging-associated epigenomic drift. The development of new bioinformatic frameworks for comparative epigenome analysis is putting epigenome maps within the reach of researchers across a wide spectrum of biological disciplines.     

Epigenetic and epigenomic variation in Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) is ideally suited for studies of natural phenotypic variation. This species has also provided an unparalleled experimental system to explore the mechanistic link between genetic and epigenetic variation, especially with regard to cytosine methylation. Using high-throughput sequencing methods, genotype to epigenotype to phenotype observations can now be extended to plant populations. We review the evidence for induced and spontaneous epigenetic variants that have been identified in Arabidopsis in the laboratory and discuss how these experimental observations could explain existing variation in the wild.     

Interindividual variation in the responses of cultured human lymphocytes to exposure from DNA damaging chemical agents: Interindividual variation to carcinogen exposure

Human population variability to standardized doses of N-acetoxy-2-acetylaminofluorene (NA-AAF) and 7,12-dimenthylbenz(a)anthracene (DMBA) was determined in cultured lymphocytes by measuring (a) differential stimulation of unscheduled DNA synthesis after 1 h induction of DNA damage by 10 μM NA-AAF, (b) the level of NA-AAF induced chromosome aberrations remaining after 8 h of DNA-repair synthesis, and (c) the level of [³H]DMBA bound to DNA after 18 h incubation of resting lymphocytes in 5 μM DMBA. All 3 parameters indicated individual variation to carcinogen exposure and were correlated to the population differences in age, sex, blood pressure and mortality rates. Males always had a greater potential to accumulate DNA-damage than did females regardless of the sampled population. DNA-damage potentials increased with increasing age, blood pressure of mortality rates. There was always proportionally greater DNA-damage potentials in the males than in females. The in vitro response of mature granulocytes to a 10 μM NA-AAF dose, as estimated by [³H]thymidine incorporation from unscheduled DNA synthesis, was much lower than lymphocyte response. Nevertheless, individual variations in granulocyte NA-AAF induced unscheduled DNA synthesis paralleled the inter-individual fluctuations observed in the lymphocyte responses to NA-AAF.     

Interindividual variation of malate dehydrogenase activity in the oyster Crassostrea virginica

Intertidal environments are dynamic, stressful niches and variation in physiological parameters may determine distribution and survival of individuals in a population. We demonstrated that mitochondria of the oyster Crassostrea virginica oxidize malate more readily than other Krebs cycle intermediates and investigated the level of interindividual variability in oyster malate dehydrogenase (MDH) activity and total protein content in muscle tissues. Both MDH activity and total protein evidenced a high level of interindividual variation in heart and adductor among a sample of more than 50 oysters. Normalization to total DNA failed to explain the variation in either MDH activity or protein content of phasic adductor and explained less than 40% of the variation in heart. This range of MDH titers defines a continuum of biochemical phenotypes important for understanding the relative selection forces operative on metabolic pathways within the muscles of the oyster.     

Interindividual variation of malate dehydrogenase activity in the oyster Crassostrea virginica

Intertidal environments are dynamic, stressful niches and variation in physiological parameters may determine distribution and survival of individuals in a population. We demonstrated that mitochondria of the oyster Crassostrea virginica oxidize malate more readily than other Krebs cycle intermediates and investigated the level of interindividual variability in oyster malate dehydrogenase (MDH) activity and total protein content in muscle tissues. Both MDH activity and total protein evidenced a high level of interindividual variation in heart and adductor among a sample of more than 50 oysters. Normalization to total DNA failed to explain the variation in either MDH activity or protein content of phasic adductor and explained less than 40% of the variation in heart. This range of MDH titers defines a continuum of biochemical phenotypes important for understanding the relative selection forces operative on metabolic pathways within the muscles of the oyster.     

Interindividual variation and consistency of migratory behavior in the Eurasian woodcock

Diverse spatio-temporal aspects of avian migration rely on relatively rigid endogenous programs.However,flexibility in migratory behavior may allow effective coping with unpredictable variation in ecological conditions that can occur during migration.We aimed at characterizing inter-and intraindividual variation of migratory behavior in a forest-dwelling wader species,the Eurasian woodcock Scolopax rusticola,focusing on spatio-temporal consistency across repeated migration episodes.By satellite-tracking birds from their wintering sites along the Italian peninsula to their breeding areas,we disclosed a remarkable variability in migration distances,with some birds flying more than 6,000 km to Central Asian breeding grounds(up to 101°E).Prebreeding migration was faster and of shorter duration than postbreeding migration.Birds moving over longer distances migrated faster during prebreeding migration,and those breeding at northernmost latitudes left their wintering areas earlier.Moreover,birds making longer migrations departed earlier from their breeding sites.Breeding site fidelity was very high,whereas fidelity to wintering areas increased with age.Migration routes were significantly consistent,both among repeated migration episodes and between pre-and postbreeding migration.Prebreeding migration departure date was not significantly repeatable,whereas arrival date to the breeding areas was highly repeatable.Hence,interindividual variation in migratory behavior of woodcocks was mostly explained by the location of the breeding areas,and spatial consistency was relatively large through the entire annual cycle.Flexibility in prebreeding migration departure date may suggest that environmental effects have a larger influence on temporal than on spatial aspects of migratory behavior.     

Interindividual variation in hypoxic ventilatory response: potential role of carotid body

There is considerable interindividual variation in ventilatory response to hypoxia in humans but the mechanism remains unknown. To examine the potential contribution of variable peripheral chemorecptor function to variation in hypoxic ventilatory response (HVR), we compared the peripheral chemoreceptor and ventilatory response to hypoxia in 51 anesthetized cats. We found large interindividual differences in HVR spanning a sevenfold range. In 23 cats studied on two separate days, ventilatory measurements were correlated (r = 0.54, P less than 0.01), suggesting stable interindividual differences. Measurements during wakefulness and in anesthesia in nine cats showed that although anesthesia lowered the absolute HVR it had no influence on the range or the rank of the magnitude of the response of individuals in the group. We observed a positive correlation between ventilatory and carotid sinus nerve (CSN) responses to hypoxia measured during anesthesia in 51 cats (r = 0.63, P less than 0.001). To assess the translation of peripheral chemoreceptor activity into expiratory minute ventilation (VE) we used an index relating the increase of VE to the increase of CSN activity for a given hypoxic stimulus (delta VE/delta CSN). Comparison of this index for cats with lowest (n = 5, HVR A = 7.0 +/- 0.8) and cats with highest (n = 5, HVR A = 53.2 +/- 4.9) ventilatory responses showed similar efficiency of central translation (0.72 +/- 0.06 and 0.70 +/- 0.08, respectively). These results indicate that interindividual variation in HVR is associated with comparable variation in hypoxic sensitivity of carotid bodies. Thus differences in peripheral chemoreceptor sensitivity may contribute to interindividual variability of HVR.     

Subunits of human sex hormone binding globulin. Interindividual variation in size

Sex hormone binding globulin (SHBG), a dimeric plasma glycoprotein with a molecular mass of about 90 kDa, was purified from healthy individuals by a rapid two-step procedure using immunoaffinity chromatography on a monoclonal antibody column followed by fast protein liquid chromatography. The individual SHBGs so isolated were pure by several criteria, and the overall yield was usually about 20% according to radioimmunoassay. The isolated SHBGs were analyzed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate which showed the SHBG isolated from most subjects to be composed of subunits of two different sizes (52 and 49 kDa) present in the approximate ratio of 10:1 (double-banded SHBG). The SHBG of the remaining subjects contained a third subunit with an estimated molecular mass of about 56 kDa (triple-banded SHBG). In this kind of SHBG, the two heavy subunits were present in approximately equal amounts, suggesting that individuals with triple-banded SHBG are heterozygotes for a genetic variant of the protein. The various subunits of SHBG were separated and individually subjected to amino-terminal amino acid sequence analysis. They all had a heterogeneous amino terminus, but since the sequences obtained seemed to be identical, the structural differences between the subunits would appear to reside in other parts of the molecules. On isoelectric focusing, both kinds of SHBG were resolved into about 10 components, all with steroid-binding activity. Differences were noted between double-banded and triple-banded SHBG, the latter having a greater abundance of acidic species. Screening of 121 healthy individuals by a procedure involving small-scale isolation of SHBG on an antibody column followed by Western blotting revealed that 20% of the subjects had triple-banded SHBG. This new variant of SHBG was found in persons of both sexes and in children as well as in adults.     

Individualization as driving force of clustering phenomena in humans

One of the most intriguing dynamics in biological systems is the emergence of clustering, in the sense that individuals self-organize into separate agglomerations in physical or behavioral space. Several theories have been developed to explain clustering in, for instance, multi-cellular organisms, ant colonies, bee hives, flocks of birds, schools of fish, and animal herds. A persistent puzzle, however, is the clustering of opinions in human populations, particularly when opinions vary continuously, such as the degree to which citizens are in favor of or against a vaccination program. Existing continuous opinion formation models predict "monoculture" in the long run, unless subsets of the population are perfectly separated from each other. Yet, social diversity is a robust empirical phenomenon, although perfect separation is hardly possible in an increasingly connected world. Considering randomness has not overcome the theoretical shortcomings so far. Small perturbations of individual opinions trigger social influence cascades that inevitably lead to monoculture, while larger noise disrupts opinion clusters and results in rampant individualism without any social structure. Our solution to the puzzle builds on recent empirical research, combining the integrative tendencies of social influence with the disintegrative effects of individualization. A key element of the new computational model is an adaptive kind of noise. We conduct computer simulation experiments demonstrating that with this kind of noise a third phase besides individualism and monoculture becomes possible, characterized by the formation of metastable clusters with diversity between and consensus within clusters. When clusters are small, individualization tendencies are too weak to prohibit a fusion of clusters. When clusters grow too large, however, individualization increases in strength, which promotes their splitting. In summary, the new model can explain cultural clustering in human societies. Strikingly, model predictions are not only robust to "noise"-randomness is actually the central mechanism that sustains pluralism and clustering.     

tRNA gene copy number variation in humans

The human tRNAome consists of more than 500 interspersed tRNA genes comprising 51 anticodon families of largely unequal copy number. We examined tRNA gene copy number variation (tgCNV) in six individuals; two kindreds of two parents and a child, using high coverage whole genome sequence data. Such differences may be important because translation of some mRNAs is sensitive to the relative amounts of tRNAs and because tRNA competition determines translational efficiency vs. fidelity and production of native vs. misfolded proteins. We identified several tRNA gene clusters with CNV, which in some cases were part of larger iterations. In addition there was an isolated tRNALysCUU gene that was absent as a homozygous deletion in one of the parents. When assessed by semiquantitative PCR in 98 DNA samples representing a wide variety of ethnicities, this allele was found deleted in hetero- or homozygosity in all groups at ~ 50% frequency. This is the first report of copy number variation of human tRNA genes. We conclude that tgCNV exists at significant levels among individual humans and discuss the results in terms of genetic diversity and prior genome wide association studies (GWAS) that suggest the importance of the ratio of tRNALys isoacceptors in Type-2 diabetes.     

Interindividual variation in abdominal subcutaneous and visceral adipose tissue: influence of measurement site.

We evaluated the influence of measurement site on the ranking (low to high) of abdominal subcutaneous (SAT) and visceral (VAT) adipose tissue. We also determined the influence of measurement site on the prediction of abdominal SAT and VAT mass. The subjects included 100 men with computed tomography (CT) measurements at L4-L5 and L3-L4 levels and 100 men with magnetic resonance imaging (MRI) measurements at L4-L5 and 5 cm above L4-L5 (L4-L5 +5 cm). Corresponding mass values were determined by using multiple-image protocols. For SAT, 90 and 92 of the 100 subjects for CT and MRI, respectively, had a difference in rank position at the two levels. The change in rank position exceeded the error or measurement for approximately 75% of the subjects for both methods. For VAT, 91 and 95 of the 100 subjects for CT and MRI, respectively, had a difference in rank position at the two levels. The change in rank position exceeded the error of measurement for 36% of the subjects for CT and for 8% of the subjects for MRI. For both imaging modalities, the variance explained in SAT and VAT mass (kg) was comparable for L4-L5, L4-L5 +5 cm, and L3-L4 levels. In conclusion, the ranking of subjects for abdominal SAT and VAT quantity is influenced by measurement location. However, the ability to predict SAT and VAT mass by using single images obtained at the L4-L5, L4-L5 +5 cm, or L3-L4 levels is comparable.     

Phenotypic diversity and epigenomic variation - The utility of mass spectrometric analysis of DNA methylation

Epigenomic variation may underlie phenotypic diversity that is not attributable to differences in genomic sequence. Such processes provide an organism the flexibility to respond to changing environmental cues within its lifetime, and perhaps its offspring's lifetime, and would therefore be expected to confer a selective advantage in evolutionary terms. Analysis of epigenomic variation within a population may be both a useful measure of developmental exposures and an indicator of future phenotype. A key molecular indicator of epigenomic variation in organisms is the chemical modification of DNA by methylation at specific nucleotide residues in the genome. Here we discuss how mass spectrometry can be utilised to provide quantitative analysis of DNA methylation patterns across populations. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.     

The functional impact of structural variation in humans

Structural variation includes many different types of chromosomal rearrangement and encompasses millions of bases in every human genome. Over the past 3 years, the extent and complexity of structural variation has become better appreciated. Diverse approaches have been adopted to explore the functional impact of this class of variation. As disparate indications of the important biological consequences of genome dynamism are accumulating rapidly, we review the evidence that structural variation has an appreciable impact on cellular phenotypes, disease and human evolution.     

Genome-wide associations of gene expression variation in humans

The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, Chromosome 21 and Chromosome 20q12–13.2. We apply three different methods of multiple test correction, including Bonferroni, false discovery rate, and permutations. For the 374 expressed genes, we find many regions with statistically significant association of single nucleotide polymorphisms (SNPs) with expression variation in lymphoblastoid cell lines after correcting for multiple tests. Based on our analyses, the signal proximal (cis-) to the genes of interest is more abundant and more stable than distal and trans across statistical methodologies. Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation. In addition, we demonstrate that the HapMap cell lines themselves may serve as a useful resource for quantitative measurements at the cellular level.     

Interindividual variation in the attractiveness of human odours to the malaria mosquito Anopheles gambiae s. s

Differences between human individuals in their attractiveness to female mosquitoes have been reported repeatedly, but the underlying mechanisms are not well understood. Skin emanations from 27 human individuals, collected on glass marbles, were tested against ammonia in a dual-choice olfactometer to establish their degrees of attractiveness to anthropophilic Anopheles gambiae s.s. Giles (Diptera: Culicidae) mosquitoes. Ammonia was used as a standard odour source because of its proven attractiveness to An. gambiae s.s. Skin emanations from most volunteers attracted significantly more mosquitoes than ammonia. There were clear differences in the attractiveness of skin emanations from different volunteers relative to that of ammonia, as well as in the strength of the trap entry response. Consistent differences were observed when emanations from the three most and the three least attractive volunteers were tested pairwise. No gender or age effect was found for relative attractiveness or trap entry response. Emanations from volunteers with higher behavioural attractiveness elicited higher electroantennogram response amplitudes in two pairs, but in a third pair a higher electroantennogram response was found for the less attractive volunteer. These results confirm that odour contributes to the differences in attractiveness of humans to mosquitoes.     

Interindividual Variation in Mitotic Recombination

Mitotic recombination (MR) between homologous chromosomes is a mutational event that results in loss of heterozygosity in half of the segregants at mitosis. Loss of heterozygosity may have important biological consequences. The purpose of this study was to describe human variation in the spontaneous frequency of MR. Using an immunoselection technique for isolating the somatic mutations that result in loss of expression of one of the codominant alleles at the HLA-A locus, we have measured the frequency and molecular basis of somatic mutations in lymphocytes from a population of young adults. Mutations were classified as being the result of intragenic changes, major deletions, or MR. Here we show that the MR mutation frequency in females was significantly greater than that in males but that intragenic mutation frequency showed no association with sex. Individual variation in MR frequency ranged over more than two orders of magnitude and was not normally distributed. Furthermore, the observed number of individuals from whom no mutants resulting from MR were obtained was significantly greater than was expected. The endogenous level of MR may be under genetic control. Given the association of loss of heterozygosity with cancer initiation and progression, low endogenous MR may confer a reduced lifetime risk of cancer, and the converse may apply.