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Thesis advisor: Michelle M. Meyer / Ribosomes play a vital role in all cellular life translating the genetic code into functional proteins. This pivotal function is derived from its structure. The large and small subunits of the ribosome consist of 3 ribosomal RNA strands and over 50 individual ribosomal proteins that come together in a highly coordinated manner. There are striking differences between eukaryotic and prokaryotic ribosomes and many of the most potent antibacterial drugs target bacterial ribosomes (e.g. tetracycline and kanamycin). Bacteria spend a large amount of energy and nutrients on the production and maintenance of these molecular machines: during exponential growth as much as 40% of dry bacterial mass is ribosomes (Harvey 1970). Because of this, bacteria have evolved an elegant negative feedback mechanism for the regulation of their ribosomal proteins, known as autoregulation. When excess ribosomal protein is produced, unneeded for ribosome assembly, the protein binds a structured portion of its own mRNA transcript to prevent further expression of that operon. Autoregulation facilitates a quick response to changing environmental conditions and ensures economical use of nutrients. My thesis has investigated the autoregulatory function of ribosomal protein S15 in diverse bacterial phyla. In many bacterial species, when there is excess S15 the protein interacts with an RNA structure formed in the 5’-UTR of its own mRNA transcript that enables autoregulation of the S15-encoding operon, rpsO. For many ribosomal proteins (ex. L1, L20, S2) there is striking homology and often mimicry between the recognition motifs within the rRNA and the regulatory mRNA structure. However, this is not the case for S15-three different regulatory RNA structures have been previously described in E. coli, G. stearothermophilus, and T. thermophilus (Portier 1990, Scott 2001, Serganov 2003). These RNAs share little to no structural homology to one another, nor the rRNA, and they are narrowly distributed to their respective bacterial phyla, Gammaproteobacteria, Firmicutes, and Thermales. It is unknown which regulatory RNA structures control the expression of S15 outside of these phyla. Additionally, previous work has shown the S15 homolog from G. stearothermophilus is unable to regulate expression using the mRNA from E. coli. These observations formulate the crux of the question this thesis work endeavors to answer: What drove the evolution of such diverse regulatory RNA structures in these different bacteria? In Chapter II, “Discover and Validate Novel Regulatory Structures for Ribosomal Protein S15in Diverse Bacterial Phyla”, I present evidence for the in silico identification of three novel regulatory RNA structures for S15 and present experimental evidence that one of these novel structures is distinct from those previously described. In Chapter III, “Co-evolution of Ribosomal Protein S15 with Diverse Regulatory RNA Structures”, I present evidence that the amino acid differences in S15 homologs contribute to differences in mRNA binding profiles, and likely lead to the development of the structurally diverse array of the regulatory RNAs we observe in diverse bacterial phyla. In Chapter IV, “Synthetic cis-regulatory RNAs for Ribosomal Protein S15”, I investigate the derivation of novel cis-regulatory RNAs for S15 and find novel structures are readily-derived, yet interact with the rRNA-binding face of S15. Together the work presented in this thesis advances our understanding of the co-evolution between ribosomal protein S15 and its regulatory RNAs in diverse bacterial phyla. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

In response to low oxygen (hypoxia), cells have evolved sophisticated gene expression programmes for survival and adaption. How the chromatin state coordinates these changes remains largely unknown. Global histone methylation changes occur in response to hypoxia, however, temporal dynamics of histone methylation changes and how they correlate with hypoxia induced gene transcription changes is ill defined. The Jumonji C (Jmjc) histone demethylases are oxygen dependent enzymes and represent a potential link between chromatin structure and oxygen sensing. Many of these enzymes are differentially expressed in hypoxia and some have been found to influence the hypoxic response. Here, the JmjC histone demethylase, KDM2B, is found to be induced at the mRNA level but not at the protein level in response to hypoxia. KDM2B was also found to regulate the transcriptional response hypoxia, in a cell type dependent manner, through control of Hypoxia Inducible Factor (HIF) subunits, HIF 1 and 2α. These findings highlight complex HIF-KDM2B crosstalk involved in the cells response to low oxygen. Additionally, it was found that various histone methylation marks are induced in the early response to hypoxia prior to hypoxia induced gene transcription changes. This demonstrates that chromatin structural marks responds rapidly to changes in oxygen availability. Furthermore the methylation landscape of 2 two active transcription histone methylation marks, H3K4me3 and H3K36me3, were mapped by ChIP sequencing in the acute response to hypoxia. This analyses found specific changes in histone methylation, which correlate with the core gene transcription changes in hypoxia, pointing towards a mechanism by which rapid chromatin changes programs the cell for hypoxic transcription. Finally, KDM5A was identified to, at least in part, regulate early hypoxia H3K4me3 changes and changes in gene expression of a subset of hypoxia responsive genes. Findings described herein provide evidence for the role of chromatin structure dynamics, mediated by chromatin modifying enzymes, in regulating the hypoxic response. Specifically, early histone methylation changes elicited in acute hypoxia may help establish a chromatin landscape for the cell to transcriptionally respond, which is essential for survival and adaptation to hypoxia. Insights into chromatin dynamics in the response to hypoxia and the role played by JmjC histone demethylases in regulating the hypoxic response has the potential for new drug discovery in diseases such as cancer, were hypoxia, epigenetics and JmjC enzymes are often implicated in disease progression.

­^¤åºK­n The main objective of this thesis is to analyze the characteristics of telecommunication regulatory structure and regulatory policy. I will analyze the telecommunication regulatory structure and telecommunication policy in Sweden, trying to find out some principles for our government in managing the development of telecommunication. The rapid transformation of the telecommunications sector has resulted in a number of important regulatory developments. There have been three major trends in the development of regulatory institutions. First, many countries have established sector specific independent regulators that are separated from line-ministries, which have the responsibility for policy making in the sector. Second, competition authorities have been given an enhanced role in the telecommunication sector as the competition has developed. Finally, some countries are beginning to take into consideration about the integration of regulatory institutions in telecommunications and in broadcasting in the light of convergence between the two telecommunication services. After understanding these trends, I will discuss and analyze Sweden¡¦s telecommunication regulatory structure. To perfect the development of the telecommunications industry depends on four integrated systems: foreign ownership, price regulation, network interconnection and universal service systems. I will open Sweden¡¦s policy in these systems for discussion.