Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

An investigation of the stresses and deflections of swept plates

The problem in this investigation was to determine the stress and deflection patterns of a thick cantilever plate at various angles of sweepback.

The plate was tested at angles of sweepback of zero, twenty, forty, and sixty degrees under uniform shear load at the tip, uniformly distributed load and torsional loading.

For all angles of sweep and for all types of loading the area of critical stress is near the intersection of the root and trailing edge. Stresses near the leading edge at the root decreased rapidly with increase in angle of sweep for all types of loading. In the outer portion of the plate near the trailing edge the stresses due to the uniform shear and the uniformly distributed load did not vary for angles of sweep up to forty degrees. For the uniform shear and the uniformly distributed loads for all angles of sweep the area in which end effect is pronounced extends from the root to approximately three quarters of a chord length outboard of a line perpendicular to the axis of the plate through the trailing edge root. In case of uniform shear and uniformly distributed loads the deflections near the edge at seventy-five per cent semi-span decreased with increase in angle of sweep. Deflections near the trailing edge under the same loading conditions increased with increase in angle of sweep for small angles and then decreased at the higher angles of sweep. The maximum deflection due to torsional loading increased with increase in angle of sweep.

The geochronology of the plutonic and metamorphic rocks of New Zealand

Extensive Rubidium-Strontium age determinations on both mineral and total rock samples of the crystalline rocks of New Zealand, which almost solely crop out in the South Island, indicate widespread plutonic and metamorphic activity occurred during two periods, one about 100-118 million years ago and the other about 340-370 million years ago. The former results date the Rangitata Orogeny as Cretaceous. They associate extensive plutonic activity with this orogeny which uplifted and metamorphosed the rocks of the New Zealand Geosyncline, although no field association between the metamorphosed geosynclinal rocks and plutonic rocks has been found. The Cretaceous plutonic rocks occur to the west in the Foreland Province in Fiordland, Nelson, and Westland, geographically separated from the Geosynclinal Province. Because of this synchronous timing of plutonic and high pressure metamorphic activity in spatially separated belts, the Rangitata Orogeny in New Zealand is very similar to late Mesozoic orogenic activity in many other areas of the circum-Pacific margin (Miyashiro, 1961).

The 340-370 million year rocks, both plutonic and metamorphic, have been found only in that part of the Foreland Province north of the Alpine Fault. There, they are concentrated along the west coast over a distance of 500 km, and appear scattered inland from the coast. Probably this activity marks the outstanding Phanerozoic stratigraphic gap in New Zealand which occurred after the Lower Devonian.

A few crystalline rocks in the Foreland Province north of the Alpine Fault with measured ages intermediate between 340 and 120 million years have been found. Of these, those with more than one mineral examined give discordant results. All of these rocks are tentatively regarded as 340-370 million year old rocks that have been variously disturbed during the Rangitata Orogeny, 100-120 million years ago.

In addition to these two periods, plutonic activity, dominantly basic and ultrabasic, but including the development of some rocks of intermediate and acidic composition, occurred along the margin of the Geosynclinal Province at its border with the Foreland Province during Permian times about 245 million years ago, and this activity possibly extended into the Mesozoic.

Evidence from rubidium-strontium analyses of minerals and a total rock, and from uranium, thorium, and lead analyses of uniform euhedral zircons from a meta-igneous portion of the Charleston Gneiss, previously mapped as Precambrian, indicate that this rock is a 350-370 million year old plutonic rock metamorphosed 100 million yea rs ago during the Rangitata Orogeny. No crystalline rocks with primary Precambrian ages have been found in New Zealand. However, Pb²⁰⁷/Pb₂₀₆ ages of 1360 million years and 1370 million years have been determined for rounded detrital zircons separated from each of two hornfels samples of one of New Zealand's olde st sedimentary units, the Greenland Series. These two samples were metamorphosed 345- 370 million years ago. They occur along the west coast, north of the Alpine Fault, at Waitaha River and Moeraki River, separated by 135 km. The Precambrian measured ages are most likely minimum ages for the oldest source area which provided the detrital zircons because the uranium, thorium and lead data are highly discordant. These results are of fundamental importance for the tectonic picture of the Southwest Pacific margin and demonstrate the existence of relatively old continental crust of some lateral extent in the neighborhood of New Zealand.

Using Earth Deformation Caused by Surface Mass Loading to Constrain the Elastic Structure of the Crust and Mantle

Surface mass loads come in many different varieties, including the oceans, atmosphere, rivers, lakes, glaciers, ice caps, and snow fields. The loads migrate over Earth's surface on time scales that range from less than a day to many thousand years. The weights of the shifting loads exert normal forces on Earth's surface. Since the Earth is not perfectly rigid, the applied pressure deforms the shape of the solid Earth in a manner controlled by the material properties of Earth's interior. One of the most prominent types of surface mass loading, ocean tidal loading (OTL), comes from the periodic rise and fall in sea-surface height due to the gravitational influence of celestial objects, such as the moon and sun. Depending on geographic location, the surface displacements induced by OTL typically range from millimeters to several centimeters in amplitude, which may be inferred from Global Navigation and Satellite System (GNSS) measurements with sub-millimeter precision. Spatiotemporal characteristics of observed OTL-induced surface displacements may therefore be exploited to probe Earth structure. In this thesis, I present descriptions of contemporary observational and modeling techniques used to explore Earth's deformation response to OTL and other varieties of surface mass loading. With the aim to extract information about Earth's density and elastic structure from observations of the response to OTL, I investigate the sensitivity of OTL-induced surface displacements to perturbations in the material structure. As a case study, I compute and compare the observed and predicted OTL-induced surface displacements for a network of GNSS receivers across South America. The residuals in three distinct and dominant tidal bands are sub-millimeter in amplitude, indicating that modern ocean-tide and elastic-Earth models well predict the observed displacement response in that region. Nevertheless, the sub-millimeter residuals exhibit regional spatial coherency that cannot be explained entirely by random observational uncertainties and that suggests deficiencies in the forward-model assumptions. In particular, the discrepancies may reveal sensitivities to deviations from spherically symmetric, non-rotating, elastic, and isotropic (SNREI) Earth structure due to the presence of the South American craton.