Title: Dynamic and temporal aspects of RNA production and processing
Description: This dissertation summarizes my work towards understanding how the intron character of genes contributes to temporal and dynamic aspects of gene expression networks and how the transcriptional and co-transcriptional aspects of gene expression are coordinated. Chapter one of my dissertation provides a background on how intron length, and the resulting large gene length, can contribute to temporal and dynamic aspects of developmentally regulated gene networks. In light of new observations and continued efforts towards the quantitative understanding of developmental networks, I revisit and comment on a perspective last presented sixteen years ago: that transcriptional delays may contribute to timing mechanisms during development (Thummel, 1992). The chapter discusses the presence of intron delays in genetic networks. In it, I consider how delays can reveal their impact at particular moments during development, which mechanistic attributes of transcription can influence them, how they can be modeled to focus on what is known and unknown, and how they can be studied using recent technological advances as well as classical genetics.

The second chapter consists of a yet unpublished manuscript outlining the results from my construction of a gene network that responds to the transcriptional times imparted by intron length. I built a synthetic network to determine whether introns could impact time delays to alter the behavior of gene networks. I show that intron lengths affect the period of time between gene expression pulses generated by delayed autoinhibition in a logically engineered negative feedback loop in animal cells. The negative feedback loop results in gene expression pulses with a broad distribution of times that increase with intron length. By reevaluating quantitative models and incorporating bursting events, from one of either two fundamentally different sources, I gain insight into what may produce the pulse distributions. Taken together, the long production time manifest in large genes alters the behavior of negative feedback loops in animal cells The third chapter consists of a study that mapped where initiating and elongating RNA polymerase accumulate across the human genome. I adapted the use of chromatin immunoprecipitation with human tiled microarrays for examining the genomic localization of RNA polymerase II. Hypophosphorylated RNA polymerase II localizes almost exclusively to 5' ends of genes. On the other hand, localization of total RNA polymerase II reveals a variety of distinct landscapes across many genes with 74% of the observed enriched locations at exons. RNA polymerase II accumulates at many annotated constitutively spliced exons, but is biased for alternatively spliced exons. The data support the perspective that a major factor of transcription elongation control in mammalian cells is the coordination of transcription and pre-mRNA processing to define exons.

The fourth chapter consists of a published manuscript describing how RNA processing machinery begins to associate at functionally consistent loci, co-transcriptionally. Using the functional-genomics approach developed in the study of RNA polymerase II, I examined three RNA processing factors that modulate discrete aspects of mRNA maturation. The major finding of this study was that factors map to the genome in distinct patterns that reflect their different processing roles. Because the RNA binding proteins did not consistently coincide with RNA Pol II, the data support a processing mechanism driven by reorganization of transcription complexes as opposed to a scanning mechanism. In sum, I present the mapping in mammalian cells of RNA binding proteins across a portion of the genome that provides insight into the transcriptional assembly of RNA-protein complexes. The final chapter of my dissertation provides a discussion of how my findings contribute to what is known about genome architecture and the machinery that interprets it during gene expression. I highlight areas and directions in the study of gene expression that will be interesting to explore in the future. (Abstract shortened by UMI.)