Dissecting the Functional Impacts of Non-Coding Genetic Variation

A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease susceptibility. Although scientists have identified genetic causes for over 4,000 monogenic diseases, the underlying mechanisms of many highly prevalent multifactorial inheritance disorders such as diabetes, obesity, and cardiovascular disease remain largely unknown. Identifying genetic mechanisms for complex traits has been challenging because most of the variants are located outside of protein-coding regions, and determining the effects of such non-coding variants remains difficult. In this dissertation, I evaluate the hypothesis that such non-coding variants contribute to human traits and diseases by altering the regulation of genes rather than the sequence of those genes. I will specifically focus on studies to determine the functional impacts of genetic variation associated with two related complex traits: gestational hyperglycemia and fetal adiposity. At the genomic locus associated with maternal hyperglycemia, we found that genetic variation in regulatory elements altered the expression of the HKDC1 gene. Furthermore, we demonstrated that HKDC1 phosphorylates glucose in vitro and in vivo, thus demonstrating that HKDC1 is a fifth human hexokinase gene. At the fetal-adiposity associated locus, we identified variants that likely alter VEPH1 expression in preadipocytes during differentiation. To make such studies of regulatory variation high-throughput and routine, we developed POP-STARR, a novel high throughput reporter assay that can empirically measure the effects of regulatory variants directly from patient DNA. By combining targeted genome capture technologies with STARR-seq, we assayed thousands of haplotypes from 760 individuals in a single experiment. We subsequently used POP-STARR to identify three key features of regulatory variants: that regulatory variants typically have weak effects on gene expression; that the effects of regulatory variants are often coordinated with respect to disease-risk, suggesting a general mechanism by which the weak effects can together have phenotypic impact; and that nucleotide transversions have larger impacts on enhancer activity than transitions. Together, the findings presented here demonstrate successful strategies for determining the regulatory mechanisms underlying genetic associations with human traits and diseases, and value of doing so for driving novel biological discovery.

Influence of Increased Human Presence in the Mills River Basin on Water Availability and Drought

Periods of drought and low streamflow can have profound impacts on both human and natural systems. People depend on a reliable source of water for numerous reasons including potable water supply and to produce economic value through agriculture or energy production. Aquatic ecosystems depend on water in addition to the economic benefits they provide to society through ecosystem services. Given that periods of low streamflow may become more extreme and frequent in the future, it is important to study the factors that control water availability during these times. In the absence of precipitation the slower hydrological response of groundwater systems will play an amplified role in water supply. Understanding the variability of the fraction of streamflow contribution from baseflow or groundwater during periods of drought provides insight into what future water availability may look like and how it can best be managed. The Mills River Basin in North Carolina is chosen as a case-study to test this understanding. First, obtaining a physically meaningful estimation of baseflow from USGS streamflow data via computerized hydrograph analysis techniques is carried out. Then applying a method of time series analysis including wavelet analysis can highlight signals of non-stationarity and evaluate the changes in variance required to better understand the natural variability of baseflow and low flows. In addition to natural variability, human influence must be taken into account in order to accurately assess how the combined system reacts to periods of low flow. Defining a combined demand that consists of both natural and human demand allows us to be more rigorous in assessing the level of sustainable use of a shared resource, in this case water. The analysis of baseflow variability can differ based on regional location and local hydrogeology, but it was found that baseflow varies from multiyear scales such as those associated with ENSO (3.5, 7 years) up to multi decadal time scales, but with most of the contributing variance coming from decadal or multiyear scales. It was also found that the behavior of baseflow and subsequently water availability depends a great deal on overall precipitation, the tracks of hurricanes or tropical storms and associated climate indices, as well as physiography and hydrogeology. Evaluating and utilizing the Duke Combined Hydrology Model (DCHM), reasonably accurate estimates of streamflow during periods of low flow were obtained in part due to the model’s ability to capture subsurface processes. Being able to accurately simulate streamflow levels and subsurface interactions during periods of drought can be very valuable to water suppliers, decision makers, and ultimately impact citizens. Knowledge of future droughts and periods of low flow in addition to tracking customer demand will allow for better management practices on the part of water suppliers such as knowing when they should withdraw more water during a surplus so that the level of stress on the system is minimized when there is not ample water supply.