Contrasting physiological requirements for T. brucei survival between procyclic (vector) and bloodstream (mammal) forms necessitate different molecular processes and therefore changes in protein expression. Transcriptional regulation is unusual in T. brucei because the arrangement of genes is polycistronic; however, genes which are transcribed together are subsequently cleaved into separate mRNAs by trans-splicing and are individually regulated. During the process of trans-splicing, a 39-nucleotide splice-leader RNA is added to the 5´ end of mRNA. In this study, gene regulation in trypanosomes will be examined in the context of the 7-methylguanosine cap attached to the 5´ end of the splice-leader. Interestingly, in addition to the capping enzymes identified in other eukaryotes, trypanosomatids have an additional guanylyltransferase and methyltransferase in the form of a bifunctional enzyme (TbCGM1). TbCGM1 was found to be essential in bloodstream form T. brucei, although the purpose of this bifunctional capping enzyme remains unclear. Null mutants of a related enzyme, monomeric methyltransferase TbCMT1, did not show an effect on cell viability in culture, however, the enzyme proved to be important for virulence in vivo. Complementary to the study of T. brucei capping enzymes, we worked to develop a method to allow structural analysis of the 5´mRNA cap by mass spectrometry. Following pre-mRNA processing, regulation of the mature mRNAs is a tightly controlled cellular process. While multiple stage-specific transcripts have been identified, previous studies using RNA-seq found that the changes in overall transcript level do not necessarily reflect the abundance of the corresponding proteins. We hypothesized that in addition to mRNA stability, mRNA recruitment to ribosomes may play a significant role in the regulation of gene expression in T. brucei. To approach this question, we performed RNA-seq of total, subpolysomal, and polysomal mRNA. This transcriptomic data was then correlated with published proteomic studies to obtain a global picture of the relative translation efficiencies and their relationship to steady-state protein levels between bloodstream and procyclic form T. brucei.

Proper mRNA nuclear export is essential for harmonious growth and maintenance of a cell. An effective weapon influenza virus employs to hijack a host cell is its ability to inhibit such export. Exactly how influenza virus achieves this inhibition is not fully known. Here, we demonstrate that upon infection, influenza virus degrades two nucleopore proteins (Nup98 and Nup96), which play a key role in mRNA nuclear export. Also, a main virulence factor of influenza virus (non-structural protein 1, NS1) binds directly to NXF1 and E1B-AP5, two key constituents of the mRNA export pathway (NXF1/NXT pathway) responsible for exporting bulk (~70%) mRNA from the nucleus. By increasing the expression levels of members of the NXF1/NXT pathway, we were able to reverse NS1-mediated inhibition of gene expression. On the other hand, by decreasing the levels of members of the NXF1/NXT pathway, we demonstrated that host cells become more sensitive to influenza virus infection and produce more viral particles. These results demonstrate undiscovered influenza-mediated host interactions that may be used to medicinally inhibit influenza virus. To this end, high-throughput screens were designed to identify small molecule antagonists of both NS1-mediated inhibition of gene expression and influenza virus-mediated cell death. Seventy-one compounds were identified, and the most potent molecule (named compound #8) was examined further. We found that compound #8 releases influenza virus-mediated mRNA nuclear export blockage and decreased viral replication and viral gene expression. Thus, the bulk mRNA nuclear export machinery is vital to antiviral response, and compound #8 enhances its ability to fight the cytopathic effects of NS1 and influenza virus. In conclusion, our data demonstrate that the mRNA export machinery is disrupted by influenza virus, and that this machinery also facilitates an antiviral function. We have also shown that these two events can be manipulated chemically to attenuate the negative effect of the virus and enhance the positive antiviral effect of the mRNA export machinery, thereby providing a powerful, new strategy against the ever-present, global threat of influenza virus.

The RNA-binding protein (RBP) and Hu/ELAV family member HuD regulates mRNA metabolism of genes that encode proteins involved in neuronal differentiation, learning and memory, and certain neurological diseases. Given the important functions of HuD in a variety of processes, we set out to characterize the 5’ genomic region of the mammalian HuD gene and determine the mechanisms that regulate its mRNA expression in neurons using P19 cells and mouse brain as models. Bioinformatic and 5’RACE (rapid amplification of cDNA ends) analyses of the HuD 5’ genomic flanking region identified eight conserved leader exons (E1s), two of which are novel. Expression of all E1 variants was established in differentiating P19 cells, mouse embryonic (E14.5) and adult brains. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in differentiating neurons. Sequential deletion of the 5’ regulatory region upstream of the predominantly expressed E1c variant revealed a well-conserved 400 bp DNA region that contains five E-boxes and is capable of directing expression of HuD specifically in neurons. Using electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitations (ChIPs), and E1c 5’ regulatory region (RR) deletion and mutation analysis, we found that two of these E-boxes are targeted by neurogenin 2 (NGN2/NEUROG2) and that this mechanism is important for induction of HuD mRNA in neurons. Additional deletion and mutation of the E1c 5’ RR revealed that putative cis-acting elements for Kruppel-like factors (KLFs) and nuclear DEAF-1-related (NuDR) transcription factors also positively regulate transcription of HuD. Together, our findings reveal that the intricate transcriptional regulation of mammalian HuD involves eight leader exons and potentially alternate promoters. We further demonstrate that transcription of HuD requires neuron-specific control by NGN2 and possibly KLF and NuDR transcription factors. To our knowledge, this is the first study to identify transcriptional events that positively regulate expression of HuD.

Cancer remains one of the most common causes for death in the world today. Researchers are continuously trying to improve old, and develop new, methods in order to strife this global problem. Much research is being made trying to find new specific biomarkers that can be used to detect and diagnose cancer in an early stage. One candidate protein for possible future use as a biomarker is tripeptidyl-peptidase II (TPPII) which has previously been shown to be up-regulated in Burkitt´s lymphoma. This paper focuses on the expression of TPPII on an mRNA-level to see if there is any difference between expression in human leucocytes from patients with a leukemia diagnosis and a healthy volunteer, in order to evaluate if the expression of TPPII have any future use as a biomarker. Patient samples were analyzed using real time qPCR, to study the expression of mRNA, and Western blot, in order to correlate the mRNA findings with protein expression. Three different cell lines with different characteristics regarding expression and function of TPPII were also used to validate the methods used and for comparison with the patient samples analyzed. A difference in expression of mRNA were seen between the different patient samples, both individually and between larger groups of samples with the same diagnosis, indicating a large individual variation, thus making future use in a clinical setting difficult. However, seeing as only a few samples were analyzed in this study, more research must be done in order to draw any final conclusions.

Friedreich ataxia (FRDA) is the most common inherited ataxia disorder, caused by a GAA repeat expansion mutation within the first intron of the FXN gene. The subsequent deficiency of frataxin protein leads to neurological disability, increased risk of diabetes mellitus, cardiomyopathy and premature death. The exact FRDA disease mechanism is not yet clear, despite some understanding of epigenetic, transcriptional and DNA repair system effects that lead to frataxin reduction. Previous studies have shown that mismatch repair (MMR) genes can affect other trinucleotide repeat disorders by destabilisation of the repeats. Furthermore, it has been proposed that frataxin deficiency might lead to cell malignancy by an as yet undefined mode of action. Therefore, the principle aim of this thesis was to use human and genetically altered mouse cells and tissues to understand the effects of MMR proteins on GAA repeat instability and FXN transcription, and also to identify potential changes in MMR transcription that might cause malignancy in FXN-defective human cells. Firstly, by using FXN and MMR genetically altered mice, MMR proteins were shown to be involved in both intergenerational and somatic GAA repeat instability, although their effects in the two systems were different. Thus, Msh2 or Msh3 were both found to protect against intergenerational transmission of GAA contractions, while loss of Msh2 or Msh3 reduced somatic GAA repeat expansions and increased levels of FXN transcription in brain and cerebellum tissues. Loss of Msh6 induced both intergenerational GAA repeat expansions and contractions, while the frequency of somatic GAA repeat expansions was reduced. Curiously, the level of FXN transcription was also reduced in Msh6-deficient brain and cerebellum tissues. On the other hand, Pms2 was found to protect against both intergenerational and somatic GAA repeat expansions, with loss of Pms2 causing increased GAA repeat expansions and decreased levels of FXN transcription in brain and cerebellum tissues. Finally, loss of Mlh1 led to a reduced frequency of both intergenerational and somatic GAA repeat expansions, but the level of FXN transcription was also reduced in brain and cerebellum tissues. Furthermore, upregulation of MMR mRNA expression was detected in human FRDA fibroblast cells, but downregulation was seen in FRDA cerebellum tissues, suggesting tissue-dependent control of FXN and MMR expression. In summary, these studies indicate that the MMR system can affect GAA repeat expansion instability and FXN transcription through different mechanisms of action. Furthermore, frataxin deficiency can also affect the levels of MMR mRNA expression in a tissue-dependent manner. These findings will assist future investigations aimed at identifying novel FRDA therapies.

Apoptosis is a tightly coordinated program to shut down and dismantle a cell, characterized by mitochondrial outer membrane permeabilization (MOMP), caspase activation to cleave hundreds of proteins, DNA fragmentation, and blocked translation. Little is known about the fate of RNA as cells die, even though apoptosis has been intensively studied for decades. Here I show that mRNAs, but not noncoding RNAs (ncRNAs), are rapidly and globally degraded during apoptosis. The decay occurs in many cell types responding to diverse apoptotic stimuli. mRNA decay is triggered early in apoptosis, preceding membrane lipid scrambling, genomic DNA fragmentation and modifications to translation initiation factors that might cause translational arrest. mRNA decay depends on MOMP and is amplified by effector caspase activity. 3' truncated mRNA decay intermediates with nontemplated uridylate-rich tails are generated during apoptosis and degraded by the 3' to 5' exonuclease DIS3L2. Knockdown of DIS3L2 reduces apoptotic mRNA decay and partially rescues cell death. I propose that global mRNA decay is a new hallmark of apoptosis caused by the concerted action of several nucleases. I also report a new role for RNA and DNA in directing cytotoxic leukocyte proteases to their substrates. When cytotoxic lymphocytes recognize and attack infected or cancerous cells, they deliver the granzyme (Gzm) serine proteases into the target cell. The Gzms cleave diverse protein substrates to orchestrate cell death. RNA binding proteins are highly enriched in unbiased proteomic screens of Gzm protein substrates. I hypothesized that the Gzms are guided to nucleic acid binding protein targets via direct binding to RNA or DNA. Using fluorescence polarization, I show that the Gzms and related leukocyte proteases bind to RNA and DNA with low nanomolar affinity. Nucleic acid binding by the Gzms facilitates their cleavage of RNA and DNA binding proteins, and guides them into target cell nuclei and onto neutrophil extracellular traps. Nucleic acid binding provides an elegant mechanism to confer protease substrate specificity for cleavage of nucleic acid-binding proteins that play essential roles in cellular gene expression and cell proliferation.

In eukaryotes, the regulation of mRNA translation and decay provides a mechanism which can be finely tuned to control gene expression. This ability to control the life cycle of an mRNA begins with the control of mRNA export from the nucleus and extends to the processes which regulate the degradation of the message. In my work, summarized below, I describe how some of the proteins involved in cytoplasmic decay regulate many aspects of the control of mRNA and also describe a novel regulatory mechanism involving the relocation of cytoplasmic mRNA back into the nucleus of the cell.Firstly, I have identified that the protein Pat1, which has been shown to be critical for translational repression and activation of decapping, consists of essentially 3 major domains. By means of a deletional functional analysis, I show that two of these domains are the primary functional domains responsible for all of the currently ascribed function of Pat1. One domain promotes translational repression and P-body assembly, while the second domain promotes mRNA decapping after assembly of the mRNA into a P-body mRNP. Along with the first evidence that Pat1 binds to RNA, we also determine numerous domain-specific interactions with mRNA decapping factors.In eukaryotic cells mRNAs are produced in the nucleus followed by what is thought to be unidirectional export to the cytoplasm. In the cytosol, mRNAs either associate with ribosomes for translation or can be found in cytoplasmic RNP granules, termed P-bodies, when they are translationally repressed. I have now demonstrated that yeast mRNAs can be re-imported into the nucleus. Import of mRNAs into the nucleus is in competition with translation and increased in strains lacking specific components of cytoplasmic processing bodies, which also exhibit nuclear-cytoplasmic shuttling. This indicates that one function of cytoplasmic granules is to limit the import of cytoplasmic mRNAs back into the nucleus. These results demonstrate a novel pathway for mRNA import into the nucleus and suggest distinct pathways of mRNA export of nascent mRNAs and imported mRNAs.

The S1 genome segment of avian reovirus is functionally tricistronic, encoding three independent protein products (named p10, p17 and ?C) from three sequential, partially overlapping open reading frames (ORFs). The dogma of translation initiation, the cap-dependent scanning model, suggests that ribosomes would normally only translate the 5?-proximal ORF. Four alternate mechanisms of translation initiation could account for translation of the downstream ?C ORF; an IRES element, reinitiation, ribosome shunting, and leaky scanning. The objective of my doctoral research was to investigate the translation initiation mechanisms that are operative on the S1 mRNA. Translation of the p10 and p17 ORFs was revealed to be coordinated via standard leaky scanning, while none of the known mechanisms of translation initiation could account for expression of the ?C ORF. Further investigation determined that two alternate cap-dependent mechanisms contribute to translation initiation at the ?C AUG codon. The first mechanism involves a modified version of enhanced leaky scanning. Although insertion of upstream elements known to impede scanning ribosomal subunits dramatically inhibited translation of the downstream ORF in the context of other mRNAs, the same elements only marginally reduced ?C translation. Specific features of the S1 mRNA therefore function to promote leaky scanning and translation of the ?C ORF. The inability to eliminate ?C expression beyond a threshold retention level of ~20-30%, despite the presence of eight upstream start codons that should eliminate leaky scanning, strongly suggests that ribosomes must also utilize a scanning-independent means to access the internal ?C start site. This mechanism for ?C translation initiation, which I termed ribosome handoff, allows ribosomes to bypass upstream elements, and requires a sequence-dependent translation enhancer element present within S1 nucleotides 366-392 that may function to mediate handoff via complementarity with 18S ribosomal RNA. Translation initiation at the ?C start site is therefore made possible by two alternative mechanisms, enhanced leaky scanning and ribosome handoff from the 5?-cap. The novelty of these two mechanisms highlights the complexity of the translation initiation process and the potential heterogeneity of cellular ribosomes, which raises the possibility that internal initiation may be far more common than currently appreciated.

Messenger RNA transcripts of αs2- and к-casein are translated at 25% of the efficiency of αs1- and β-casein transcripts; however, the molecular mechanisms governing the difference are unknown. We hypothesized that the bovine casein translational efficiency is influenced by characteristics of the untranslated regions (UTRs) and coding regions. The main objective of this study was to identify molecular mechanisms that explain differential translational regulation between bovine β- and αs2-casein by assessing the role of each putative translational regulatory factor found throughout full-length sequences in both in cellular and cell-free translation systems. This dissertation begins with the cloning and initial characterization of bovine β- and αs2-casein. Transcript analysis indicates that the two genes share similar characteristics of nucleotide sequence around the coding region and secondary structure. It is confirmed that αs2-casein mRNA has a lower translational efficiency compared to that of β-casein in a cell-free system. The latter portion of this thesis investigates further the UTRs and codon usage effect on difference in translational efficiency between β- and αs2-casein. Overall, our data suggest that β-casein 3’ UTR and αs2-casein 5’ UTR exert stimulatory effects on translation yet their effectiveness depends on the upstream and downstream sequences with which they are associated. Replacement of the UTRs of αs2-casein mRNA with those of β-casein did not stimulate translation. A stronger effect on translational efficiency was found in the coding region of αs2-casein which displays unfavourable codons at the 3’ terminus. Deletion of a 28-codon fragment from the 3’ terminus of the αs2-casein coding region increased translation to a par with β-casein. We suggest that the last 28 codons of αs2-casein is the main regulatory sequence that attenuates its expression and is responsible for the different translational expression of β- and αs2-casein mRNAs. Identification of regulatory factors that are responsible for translation efficiency improves our understanding of the molecular mechanisms of control of milk protein prodiction in secretory cells of the bovine mammary glands. / NSERC canada

RNA molecules isolated from FFPE samples are highly fragmented and modified, and generally deemed unsuitable for downstream gene expression profiling. With the development of molecular biology, there has been growing interest in profiling archival FFPE samples. Successful profiling of transcripts from FFPE samples would greatly expand tissue sources for large scale gene expression studies; also it would pave the way for future applications on the type of tissue readily available in the clinical setting. So far, there is a lack of systemic studies evaluating the quality of RNA isolated from routinely processed FFPE samples, and it has remained difficult to assess how well FFPE-derived RNA mirrors the status of RNA isolated before fixation. In this project, the similarity of miRNA and mRNA profiles between matched frozen and FFPE lymphoid hyperplasia tissues (N=7 for miRNA comparison, N=4 for mRNA comparison) were evaluated. We found consistently good correlation (mean of Pearson coefficient=0.939, mean of Spearman coefficient=0.905, mean of Kendall tau=0.744) between matched frozen and FFPE-derived miRNA profiles, suggesting FFPE samples may retain miRNA expression information quite well. This has major positive implications for research using FFPE samples, as miRNA profiling becomes more prominent in bioprofiling studies. On the contrary, mRNA isolated from FFPE samples showed less correlation (Spearman coefficient less than 0.75) with its frozen counterpart on the Agilent microarray platform. With a post extraction heat treatment aimed at reversing base modifications and cross linking structures, obvious global mRNA quality improvement was observed in cases where samples appeared to be heavily cross linked, but was less effective and even detrimental in cases where cross linking was less prominent. This research suggests that the extent of cross linking may be critical in terms of determining whether a particular FFPE tissue will become a useful source of mRNA for global profiling studies / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2008-09-26 10:49:50.044