Thesis (Ph. D.)--Drexel University, 2007. / Includes abstract and vita. Includes bibliographical references (leaves 94-110).

Thesis (Ph. D.)--Case Western Reserve University, 2007. / [School of Medicine] Department of Biochemistry. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Magister Scientiae - MSc (Biochemistry) / Alternative RNA splicing is one of the leading mechanisms contributing towards transcript and protein diversity. Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. All mouse, skipped exons were observed to have ubiquitous tissue expression. Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. Our hypothesis contradicts with a previous study by Brett et al.2002, in which the authors claim that mouse and human alternative splicing is comparable. Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. The quality of the current mouse genomic data is higher than the one utilized in this study. The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves. / South Africa

La protéine tau est une protéine neuronale associée aux microtubules. L’exon 10 code pour un domaine de liaison aux microtubules et son épissage alternatif définit deux types d’isoformes ayant une fonction biologique distincte. En effet, quand l’exon 10 est exclu, les isoformes de tau ont trois domaines de liaison aux microtubules (Tau3R) alors que les isoformes en possèdent quatre lorsque l’exon 10 est inclus (Tau4R). Ainsi, les isoformes Tau4R sont connues pour avoir une meilleure affinité pour les microtubules, et permettent de mieux les stabiliser au sein de l’axone des neurones. Les tauopathies sont des maladies neurodégénératives qui se caractérisent par la présence d’agrégats de la protéine tau sous forme hyperphosphorylée. Parmi ces agrégats, certains sont composés des isoformes Tau3R et Tau4R, alors que d’autres sont essentiellement composés soit des isoformes Tau3R, soit des isoformes Tau4R. Ces données montrent qu’un défaut d’épissage alternatif de l’exon 10 de tau peut conduire à une pathologie. Cependant, la régulation de l’épissage alternatif de l’exon 10 est encore mal connue à la fois dans un contexte physiologique et pathologique et l’absence de données sur la physio-pathologie des tauopathies et de modèles d’études intégrés rendent l’avancement des connaissances et le développement de stratégies thérapeutiques nébuleux. De manière intéressante, il existe un changement d’épissage alternatif de l’exon 10 au cours du développement du cerveau chez la souris. En effet, les isoformes Tau3R sont majoritaires dans les premiers stades du développement et ne sont plus du tout exprimées à l’âge adulte. En revanche, le cerveau humain à l’âge adulte exprime autant d’isoformes Tau3R que d’isoformes Tau4R. Nous avons remarqué que deux évènements ont lieu simultanément au cours du développement du cerveau chez la souris : le changement d’expression des isoformes de tau et la mise en place de la thermogénèse. Plusieurs études ont montré que la température influence le niveau de phosphorylation de la protéine tau, mais aucune n’a mis en évidence l’impact de la température sur l’épissage alternatif de tau. Ainsi, notre hypothèse de départ est que la température représente un nouveau régulateur de l’expression des isoformes de tau, en modulant l’épissage alternatif de l’exon 10. Les principaux objectifs de cette thèse étaient d’analyser l’impact de la température sur l’épissage alternatif de l’exon 10 de tau et les mécanismes cellulaires associés aux changements d’épissage alternatif de l’exon 10. Dans un premier temps, nous avons utilisé le développement du cerveau chez la souris comme modèle pour faire une caractérisation plus précise de l’expression des isoformes de tau. Ensuite, nous avons utilisé des cultures de neurones primaires de souris, dans le but d’évaluer l’impact de changements directs de température sur l’expression des isoformes de tau. Dans un deuxième temps, nous avons utilisé une approche in vitro, pour caractériser les changements d’épissage alternatif de l’exon 10 de tau au niveau de l’ARNm et protéique. Dans un troisième temps, nous avons analysé les mécanismes cellulaires responsables de ces changements d’expression. Nos résultats montrent que la température affecte directement l’épissage alternatif de l’exon 10 au niveau de l’ARNm mais également des protéines synthétisées. De plus, nous avons vu que l’hypothermie favorise l’exclusion de l’exon 10, ce qui conforte notre observation de départ en lien avec le développement du cerveau chez la souris, tandis que l’hyperthermie favorise l’inclusion de l’exon 10 dans tous les modèles analysés. Nous avons également montré que la température affecte l’épissage alternatif de l’exon 10 humain. Nos résultats montrent également que la température affecte le patron développemental d’expression des isoformes de tau. De plus, nos résultats ciblent le facteur d’épissage Muscle blind-like (MBNL), comme mécanisme cellulaire responsable des changements d’expression des isoformes de tau induits par la température. De manière préliminaire, nos travaux de recherche montrent ainsi un nouveau rôle de la température dans la régulation de l’expression des isoformes de tau. Les prochaines étapes seraient d’évaluer l’impact fonctionnel de ces changements d’expression de tau sur le cerveau et de tester les changements de température comme nouvelle avenue thérapeutique pour le traitement des tauopathies présentant un défaut d’épissage alternatif de l’exon 10 de tau. / Tauopathies are a group of neurodegenerative disorders characterized by the presence of aggregates of hyperphosphorylated tau protein. These aggregates are either constituted of the six tau isoforms, or Tau4R isoforms or Tau3R isoforms, suggesting that altered tau exon 10 alternative splicing can lead to neurodegeneration. This was further supported by the discovery of mutations on matp gene mainly responsible for fronto-temporal dementia. The regulation of tau exon 10 alternative splicing is not fully understood in both physiological and pathological conditions. Indeed, the lack of data on the development of sporadic tauopathies (in absence of tau mutations) and models to study them make therapeutics strategies compromised. Interestingly, changes of tau isoforms expression has been reported during the mouse brain development. Indeed, Tau3R isoforms are dominant in the first developmental stages (embryonic and early post-natal) and are absent in adulthood. To the opposite, human adul brain expresses both Tau3R and Tau4R to equal amount. This inter-species fundamental difference of expression of tau isoforms is not understood. We noctided that some events are concomitant during the mouse brain development: shift of tau isoforms, shift of tau phosphorylation state and pups thermoregulation efficiency. It has been reported that temperature can influence the phosphorylation of tau protein and especially that hypothermia increases it. To date, no study has shown the impact of temperature on tau exon 10 alternative splicing. Thus, our hypothesis is that temperature is a new regulator of the expression of tau isoforms by modulating the alternative splicing of tau exon 10. The major goals of this thesis were to analyze the impact of temperature on the alternative splicing of tau exon 10 overall, and especially during the mouse brain development. On another hand, we want to analyze the mechanisms responsible for temperature-mediated tau exon 10 alternative splicing changes. First, we used the mouse brain development to characterize the expression of tau isoforms. Thus, we used mouse primary neuronal cells in the aim of analyzing the impact of direct changes of temperature on tau isoforms expression. Second, we used in vitro approaches to characterize the impact of temperature on tau exon 10 alternative splicing at both mRNA and proteins levels. Third, we have analyzed mechanisms involved in these changes. Our results show that temperature directly affects tau exon 10 alternative splicing at both mRNA and protein levels. For the first time, we show that hypothermia induces tau exon 10 exclusion whereas hyperthermia favors exon 10 exclusion. Moreover, we show that temperature is able to modulate the alternative splicing of human tau exon 10. Our results with primary neuronal cells show that temperature can influence the developmental pattern of expression of tau isoforms, suggesting that temperature is a strong modulator of tau exon 10 alternative splicing. Eventually, our results highlight the role of Muscle blind-like proteins (MBNL) as potential mechanisms involved in the regulation of tau exon 10 alternative splicing by the temperature. Interestingly, our work put in relief a new role of the temperature in the regulation of tau isoforms expression. As perspectives, it should be important to evaluate the functional impact of temperature-mediated changes of tau isoforms expression on brain.

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O veneno de Bothops jararaca contém uma série de componentes, entre eles as metaloproteinases hemorrágicas jararagina e bothropasina. Os cDNAs dessas toxinas mostram 97% de identidade. As diferenças, distribuídas ao longo de seus cDNAs, sugerem que estes mRNas não resultam de splicing alternativo. O objetivo deste trabalho foi caracterizar os genes codificadores da jararagina e bothropasina pela identificação de exons e introns no DNA genômico. DNA foi extraído do sangue de um exemplar de B. jararaca; os primers para PCR foram baseados nos cDNAs publicados. Os produtos de amplificação foram clonados e seqüenciados revelando a sequência dos genes TOX1 com 12535 pb e TOX2 com 12268 pb. Quatorze exons e treze introns foram identificados em ambos os genes. Comparação entre as sequências mostrou pontos de mutação, inserções e deleções nos exons, e principalmente nos introns dos dois genes. Este constitui o primeiro relato na literatura sobre a identificação de exons e introns nos genes codificadores de jararagina e bothropasina. / The Bothops jararaca venom contains a number of components, including hemorrhagic metalloproteinases as jararhagin and bothropasin. The cDNA of these toxins show 97% identity. The differences distributed along the cDNAs length suggest that these mRNAs do not result from alternative splicing. This study aimed to characterize the genes that encode for jararhagin and bothropasin through the identification of exons and introns in genomic DNA. DNA was extracted from the blood of a B. jararaca specimen; PCR primers were based on published cDNA sequences. Amplification products were cloned and sequenced revealing the TOX1 gene is about 12,535 bp long, and TOX2 is 12,268 bp. Fourteen exons and thirteen introns were identified in both genes. Comparison of the sequences showed point mutations, insertions and deletions in exons, and particularly in introns. This is the first report in the literature on the identification of exons and introns in genes encoding for jararhagin and bothropasin.

O veneno de Bothops jararaca contém uma série de componentes, entre eles as metaloproteinases hemorrágicas jararagina e bothropasina. Os cDNAs dessas toxinas mostram 97% de identidade. As diferenças, distribuídas ao longo de seus cDNAs, sugerem que estes mRNas não resultam de splicing alternativo. O objetivo deste trabalho foi caracterizar os genes codificadores da jararagina e bothropasina pela identificação de exons e introns no DNA genômico. DNA foi extraído do sangue de um exemplar de B. jararaca; os primers para PCR foram baseados nos cDNAs publicados. Os produtos de amplificação foram clonados e seqüenciados revelando a sequência dos genes TOX1 com 12535 pb e TOX2 com 12268 pb. Quatorze exons e treze introns foram identificados em ambos os genes. Comparação entre as sequências mostrou pontos de mutação, inserções e deleções nos exons, e principalmente nos introns dos dois genes. Este constitui o primeiro relato na literatura sobre a identificação de exons e introns nos genes codificadores de jararagina e bothropasina. / The Bothops jararaca venom contains a number of components, including hemorrhagic metalloproteinases as jararhagin and bothropasin. The cDNA of these toxins show 97% identity. The differences distributed along the cDNAs length suggest that these mRNAs do not result from alternative splicing. This study aimed to characterize the genes that encode for jararhagin and bothropasin through the identification of exons and introns in genomic DNA. DNA was extracted from the blood of a B. jararaca specimen; PCR primers were based on published cDNA sequences. Amplification products were cloned and sequenced revealing the TOX1 gene is about 12,535 bp long, and TOX2 is 12,268 bp. Fourteen exons and thirteen introns were identified in both genes. Comparison of the sequences showed point mutations, insertions and deletions in exons, and particularly in introns. This is the first report in the literature on the identification of exons and introns in genes encoding for jararhagin and bothropasin.

Thesis (Ph. D.)--West Virginia University, 2006. / Title from document title page. Document formatted into pages; contains xi, 183 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

Pre-mRNA molecules in humans contain mostly short internal exons flanked by long introns. To explain the removal of such introns, recognition of the exons instead of recognition of the introns has been proposed. This thesis studies this exon definition mechanism using a bottom-up approach. To reduce the complexity of the system under study, this exon definition mechanism was addressed using designer exons made up of prototype sequence modules of our own design (including an exonic splicing enhancer or silencer). Studies were performed in vitro with a set of DEs obtained from random combinations of the exonic splicing enhancer and the exonic splicing silencer modules. The results showed considerable variability both in terms of the composition and size of the DEs and in terms of their inclusion level. To understand how different DEs generated different inclusion levels, the problem was divided into understanding separately parameters varied between DEs. Subsequent studies focused on each of three parameters: size, ESE composition and ESS composition. The final objective was to be able to combine their effects to predict the inclusion levels obtained for the "random" DEs mentioned previously. To complement this experimental approach an equation was generated in two stages. First a general "framework" equation was obtained modeling a necessary exon definition complex that enabled commitment to inclusion. This equation used rates for the formation and dissociation of this complex without elaborating on the details for how those rates came about. In the second stage, however, formation and dissociation were modeled using novel but intuitive ideas and these models were combined into a final equation. This equation using the single-parameter perturbation data obtained previously performed well in predicting the inclusion levels of the "random" DEs. Additionally, both the final equation and the mechanisms proposed align well with results published by other groups. In order to make these results more accessible and to open more opportunities to extend them, an initial attempt is presented to identify the proteins involved in the functionality observed for each of the sequences used.

The human androgen receptor (hAR) is a ligand-activated, nuclear transcription factor. Mutations affecting the formation and/or action of the hAR cause androgen insensitivity syndrome (AIS). The majority of mutations identified to date are within the DNA- and hormone-binding domains; very few have been identified in the transactivational modulatory domain, encoded by exon 1. This work presents an analysis of exon 1 and the 5$ sp prime$-flanking region of the hAR in a set of subjects whose AIS was believed to be caused by a mutation within these regions. Six of twelve strains had a nonsense or frameshift mutation in exon 1; a seventh strain had two missense and one silent substitution; no mutations were identified in the remaining subjects. The two missense mutations were recreated, individually and together, in an hAR complementary DNA (cDNA) expression vector and expressed in heterologous COS-1 cells. Their pathogenicity could not be proven with the system and assays used. In addition, mRNA and protein levels were analyzed and correlated with the identified mutations and the subjects' phenotype.