The transcription efficiency of transfer RNA genes is modulated by sequences contained in their 5'-flanking region. For a tRNA val₄ gene a pentanucleotide with the sequence TCGCT was identified between positions -33 and -38. I have previously proposed that this sequence may be involved in specifically determining the rate of transcription of this gene. A general form of this sequence, TNNCT was found associated with other Drosophila tRNA genes which showed high ill vitro transcription efficiency. To further elucidate the role of TCGCT in tRNA transcription, single and double base-pair changes were created in the sequence TCGCT using site-specific mutagenesis. Mutations in the nucleotides -38T, -35C and -34T showed decreased levels of transcription whereas nucleotide changes at the nucleotides -37C and -36G did not reduce template activity. Therefore the sequence which modulates transcription of the tRNAVal₄ gene does have the general form TNNCT. Competition experiments between the Val₄ mutant -38G.-35A and a tRNASer₇ gene showed the TNNCT mutant to be a better competitor for transcription than the wild type template. Experiments analyzing the time-course of transcription, the effects of temperature and the effects of ionic strength indicated that TNNCT was not involved in determining the efficiency of stable complex formation. It is proposed that the pentanucleotide is probably responsible for influencing the rate of initiation of transcription. A sequence TGCCT contained in the anticodon stem/loop region of the Val₄ gene was also mutagenized and shown to be involved in complex stability or the elongation of Val₄ tRNAs. Using deletion analysis of the 5'-flanking sequences of a tRNASer₇ gene, a second positive transcription regulatory element was delimited. This sequence was also found in the 5'-flanks of the tRNAVal₄ and a tRNAArg gene. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

The nucleotide sequence of the single Drosophila meianogaster tRNA gene contained in the recombinant plasmid, pDtl20R was determined by the Maxam and Gilbert method. This plasmid hybridizes to the 90 BC site on the Val Drosophila polytene chromosomes, a minor site of tRNA4 hybridization. The Val nucleotide sequence of the tRNA4 gene present in pDtl20R differs at four Val positions from the sequence expected from that of tRNA4 . The four differences occur at nucleotides 16, 29, 41 and 57 in the coding region. Comparison of the DNA sequence of pDtl20R to that of the plasmid pDt92R, which also hybridizes to the 90 BC site, indicates that the Drosophila fragments contained in these two plasmids are either alleles or repeats. The implications of these findings are discussed. An in vitro transcription system was developed from a Drosophila Schneider II cell line. This homologous cell-free extract support specific and accurate transcription of various Drosophila tRNA Val genes. The major product of transcription is a tRNA precursor which is processed to a tRNA sized species. Transfer RNA valine genes originating from different sites on the Drosophila chromosomes are transcribed at different rates. Comparison of the sequences in the internal promoter regions of the various genes indicates that the few differences within the coding regions may not be responsible for the observed difference in the rates of transcription. This conclusion is substantiated by studies with hybrid genes constructed during the course of this work. Preliminary evidence indicates that the Val tRNA gene which is transcribed at the highest rate may be preceded in its 5'-flanking region by a positively modulating sequence. Val The precursor RNAs directed by various tRNA genes are also processed at different rates. Transcription and processing experiments with hybrid genes suggest that nucleotide changes within the coding region, which do not affect the rate of transcription, influence the rate of processing. Time course and competition experiments demonstrate that at least two kinetic steps are required for the formation of a stable transcription complex. Studies with an in vitro constructed mutant missing in nucleotides 51-61 in the tRNA coding region suggests that this deleted region (which is highly conserved in eukaryotic tRNAs) may be involved in the primary interaction required for tRNA gene transcription. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Injury, aging, and congenital disabilities of the muscular and neural systems impose a significant burden on patients and their families. Due to the tissue’s limited regenerative capacity, effective treatment interventions for restoring progressive damage is still lacking. Cell replacement therapy is primarily limited by the restricted supply of viable donor cells and variable graft survival. For addressing these limitations, we propose new strategies to obtain a target cell of interest from an autologous cell source. Herein, we engineer cell fate decisions by 1) harnessing host microenvironment and the CRISPR/dCas9-mediated transcriptional activation system to promote myogenesis of human endothelial progenitor cells (EPCs); and 2) employing substrate-mediated biophysical cues with soluble factors (biochemical cues) to drive cell commitment to neuronal lineages. For the first strategy, we hypothesized that therapeutic cells could be obtained in situ by employing the CRISPR/dCas9 system to engineer cell fate in the host tissue. Using this system, we transactivated MYOD1, a master regulator for myogenesis, to directly reprogram primary EPCs to skeletal myoblasts (SkMs). EPCs were chosen as a cell source for their easy accessibility, high proliferation, and potential contribution to regenerate vasculature and musculature tissue. The early myogenic commitment of EPCs was confirmed in vitro by MYOD1 expression, which yielded a 230-fold higher induction than the original EPCs. These cells were then transplanted for assessing their therapeutic efficacy in myotoxin-induced muscle injury model in immunodeficient mice. A one-month post-injury study resulted in the integration of induced SkMs to the injured host tissue, promotion of neoangiogenesis, and reduction in fibrotic scar formation. These findings indicate that CRISPR/Cas9-mediated target gene activation can be achieved in situ to accelerate muscle regeneration after myotoxin-induced damage. For the second strategy, we utilized both soluble and insoluble factors to convert the cell fate of neural stem/progenitor and somatic cells to various neuronal lineages, including motor neurons (MNs) and dopaminergic (DA) neurons. For soluble factors, cells were exposed to various biochemical factors, inspired by the neuronal niche environs during the natural developmental process. For insoluble factors, the conductive graphene substrate was used to support the endogenous electrical signal between neurons for enhancing the neuronal phenotypes and their functionality. We postulated that exposing the cells to these collective stimuli in vitro can alter their intrinsic signaling pathway to tailor their fate to neuronal lineages. To test the hypothesis, neural stem/progenitor and somatic cells were cultured on various substrates with or without electroactive graphene and aligned patterns. After two weeks to one month of cell fate induction in the chemically defined conditions, our results implied that cell adhesion, survival, neurite outgrowth, and maturation were facilitated on the electroactive substrates with aligned patterns compared to the control platforms. Taken together, our results in this dissertation demonstrate the feasibility of tailoring the donor cell fates within or across the germ layers. We achieved this by employing a transcriptional gene activation system and tunable microenvironmental cues elicited by soluble (chemical and growth factors) and insoluble (physical cues from the substrate) factors. Utilizing such strategies hold great promise for elucidating the optimal conditions to guide cell fate to target lineages. This work provides a rational basis for establishing a robust protocol and an in vitro culture platform to module cell fate decisions that could help realize the autologous cell-based therapy for muscular and neurodegenerative diseases.

The primary focus of this study was on the characterization of the 122 nucleotide 5' Untranslated Region (UTR) of the Alcohol Oxidase I (AOXI) gene in Pichia pastoris. The 5' UTR influences the expression of many heterologous proteins in P. pastoris. However, no systematic analysis has ever been performed on this region to date. Several truncated versions of the 5' UTR were constructed using the QuikChange II XL Site Directed Mutagenesis Kit from Stratagene, PCR, and primers designed for a distinct region. Deletions of 21, 25, 30, 43, 61, 78, and 95 nucleotides were done to the 5' UTR. Elongated versions of the 5' UTRs were constructed where fragments of 10, 20, 30, 33, 36, 40, 45, and 50 nucleotides were inserted into the vector, subsequently increasing the length of the 5' UTR. All constructs were assessed using the β-galactosidase activity assay to determine if various constructs led to an increase or decrease in the rate of translation. Deletions had a variable effect on β-galactosidase expression, whereas additions decreased expression but not in a linear fashion. Final confirmation was performed using Northern analysis to ensure that the effects were due to translation rates and not nRNA transcription or degradation.

Little is actually known about the transcriptional regulation of spider silk as most studies have focused on the material properties of silks. We isolated and mapped the TuSp1 core promoter from the black widow spider, Latrodectus hesperus. Using a genomic DNA walking strategy, we have isolated an upstream segment (581 bp) of genomic DNA containing the promoter as well as the first exon of the TuSp1 gene. This upstream regulatory element was able to initiate transcription in insect cells when placed upstream the promoterless firefly luciferase reporter gene. Initiation of transcription was orientation dependent, as insertion of this upstream regulatory module in the reverse orientation led to inefficient transcriptional initiation. Only 170 bp of upstream sequence was required for strong transcriptional initiation, showing that core promoter resides within the first 170 bp of upstream 5' -flanking DNA. We also demonstrate the bHLH factor SGSF1 can repress gene transcription of the TuSp1 core promoter, implying SGSF I might participate in the transcriptional regulation of the TuSp1 gene in vivo.

ABF -1 is a human class II bHLH transcription factor that is expressed predominantly in activated B cells and EBV immortalized cell lines. A portion of this study sought to characterize the homolog of ABF- l in Caenorhabditis e/egans. The nematode gene product, ceABF -1, is capable of forming heterodimers with E2A gene products and binding E box binding sites. HeLa cells transfected with ceABF-1 reveal that it is capable of blocking E2A mediated gene transcription. In order to maintain full repression capabilities, two conserved amino acid residues within helix I ofthe HLH domain are required. These results show a conserved mechanism of gene repression between invertebrates and vertebrates. This study also sought to analyze ABF-1 mediated regulation of both ld3 and cellular growth. Using a human ABF-1 stably transfected cell line, ID3 protein levels and transcript levels were shown to increase in response to overexpression of ABF-1 via western and northern blot, respectively. Flow cytometry analysis and Real-time PCR revealed that ABF-1 programs a slow down in the cell cycle, however this growth arrest is not mediated by ID3.

The methylotrophic yeast, Pichia past oris, is one of the most respected and widely used systems today. The ability of this yeast to produce large masses of protein and metabolize methanol as a sole source of carbon and energy is attributed to the highly induceable Alcohol Oxidase I promoter (AOXI). Despite of the disperse popularity and use of this promoter over the last 15 years, little is known about the transcription controls at a molecular level. A 5'>3' deletion analysis of the AOXI promoter was perrormed to gain understanding of the promoter's regulation and provided insight to the approximate locations of the important regulatory regions. A total of 10 truncations were made unveiling two areas ofhigh activity located between positions, -257 to-235, and, -235 to -188. In addition, a 14-base pair internal deletion was made between positions, -215 to -201. This region was shown to be necessary for transcriptional activation by deletion analysis. Sufficiency studies suggested that this 14-base pair element could serve as an activator sequence in both glucose and methanol.

While development in flies is well understood, pattem formation and the evolution thereof in arachnids have yet to be clarified. Flies and other metazoans primarily use two families of genes called Hox genes and Pax genes to regulate embryogenesis. Because of the high evolutionary conservation of Hox and Pax proteins, I hypothesize that arachnids also use this system to organize their body pattern. To enable studies of the Westem black widow spider, Latrodectus hesperus, an embryonic eDNA library and a fixation protocol were developed for L. hesperus embryos. The generation of these tools will allow comprehensive analysis of black widow spider development and give insight into whether, and how, spiders use Hox and Pax genes to organize their bodies. Finally, it will provide a more thorough understanding of how different developmental mechanisms have evolved and ultimately how changes in gene expression can lead to a change in overall body plan.

Assessing the functional impact of genetic variants across the human genome is essential for understanding the molecular mechanisms underlying complex traits and disease risk. Genetic variation that causes changes in gene expression can be analyzed through parallel genotyping and functional genomics assays across sets of individuals. In particular, regulatory variants may impact transcription factor regulation. In this thesis, to map variants that impact the expression of many genes simultaneously through a shared transcription factor (TF), we use an approach in which the protein-level regulatory activity of the TF is inferred from genome-wide expression data and then genetically mapped as a quantitative trait. In Chapter 2, we developed a generalized linear model (GLM) to estimate TF activity levels in an individual-specific manner, and used it to analyze RNA-seq profiles from the Genotype-Tissue Expression (GTEx) project. A key feature is that we fit a beta-binomial GLM at the level of pairs of neighboring genes in order to control for variation in local chromatin structure along the genome and other confounding effects. As a predictor in our model, we use differential gene expression signatures from TF perturbation experiments. After estimating genotype-specific activities for 55 TFs across 49 tissues, in Chapter 3, we performed genome-wide association analysis on the virtual TF activity trait. This revealed hundreds of TF activity quantitative trait loci, or aQTLs, highlighting the potential of genetic association studies for cellular endophenotypes based on a network-based multi-omic approach. Lastly, in Chapter 4, we studied the direct impact of genetic variants on TF binding by predicting genetic effects on TF binding affinity. Specifically, we predicted binding affinity on allele-specific binding data using TF binding models derived by the ProBound recently developed by our laboratory, and constructed a likelihood model to assess the performances across different binding models. This indicates that ProBound provides a promising tool for the prediction of genetic effects on in vivo TF binding.

Indiana University-Purdue University Indianapolis (IUPUI) / The Grr1 (Glucose Repression Resistant) protein in Saccharomyces cerevisiae is an F-box protein for the E3 ubiquitin ligase protein complex known as the SCFGrr1 (Skp, Cullin, F-box). F-box proteins serve as substrate receptors for this complex and in this capacity Grr1 serves to promote the ubiquitylation and subsequent proteasomal degradation of a number of intracellular protein substrates. Substrates of SCFGrr1 include the G1-S phase cyclins, Cln1 and Cln2, the Cdc42 effectors and cell polarity proteins, Gic1 and Gic2, the FCH-bar domain protein, Hof1, required for cytokinesis, the meiosis activating serine/threonine protein kinase, Ime2, the transcriptional regulators of glucose transporters, Mth1 and Std1, and the mitochondrial retrograde response inhibitor Mks1. Stabilization of these substrates lead to pleiotrophic phenotypic defects in grr1Δ strains including resistance to glucose repression, accumulation of grr1Δ cells in G2 and M phase of the cell cycle, sensitivity to osmotic stress, and resistance to divalent cations. However, many of these phenotypes are not reflected at the gene expression level. We conducted a quantitative genomic vii and proteomic comparison of 914 loci in a grr1Δ and wild-type strain grown to early log-phase in glucose media. These loci encompassed 16.7% of the Saccharomyces proteome of which 22.3% exhibited discordance between gene and protein expression. GO process enrichment analysis revealed that discordant loci were enriched in the processes of “trafficking”, “mitosis”, and “carbon/energy” metabolism. Here we show that these instances of discordance are biologically relevant and in fact reflect phenotypes of grr1Δ strains not evident at the transcriptional level. Additionally, through combined biochemical and network analysis of discordant loci among “carbon and energy metabolism” we were able to not only construct a model for central carbon metabolism in grr1Δ strains but also were able to elucidate a novel molecular event that may serve to regulate glucose repression of genes needed for respiration in response to changes in glucose concentration.