Transposons were first discovered as "jumping genes" by Barbara McClintock, who continued to study them in maize through the 1940's and 1950's. Since then, transposons have been shown to make up a large percentage of eukaryotic genomes, including close to half of the human genome, but have been dismissed as simply "junk DNA." Recently, the importance of keeping transposons tightly regulated within the cellular environment has begun to be appreciated; the mechanisms to accomplish this have been studied and the current understanding of pathways governing transposon regulation is discussed within this dissertation. However, recent work presented within the scope of this dissertation in Drosophila melanogaster revealed a previously unknown function for condensin complexes in transposable element regulation. These studies provide a link between pathways governing chromosome pairing and transposon regulation. The potential interplay between these two pathways is intriguing and until now, largely unexplored.Aside from how transposons themselves are regulated, studies into potential roles they may play in the regulation of other protein coding genes within the cell may provide clues into the functionality of these elements within our genome. As a specific example, BRCA1 has a high density of retrotransposon sequences within its primary transcript, and studies of BRCA1 regulation presented within this dissertation has led to the development of a model for a novel gene regulatory mechanism occurring in human cells involving retrotransposons. This mechanism may provide direct relevance to cancer etiology, as retrotransposons have long been known to be misregulated in cancer.As a sum, the work presented within this dissertation extends our knowledge of how transposons are regulated and provides some of the first evidence for their functionality in gene regulatory pathways within human cells.

Reproduction de : Thèse de doctorat : Biologie : Le Mans : 2006. / Titre provenant de l'écran-titre. Bibliogr. f. 150 - 176.

There are two full length variants of the Pokey DNA transposon, PokeyA and PokeyB, and two MITEs, mPok1 and mPok2. Pokey inserts into ribosomal DNA (rDNA) and other genomic locations within the genomes of Daphnia species. I used qPCR to estimate haploid rDNA and Pokey copy number in five Daphnia pulex complex species. In general, rDNA number ranges from ~100 to 500. In four species, low numbers of PokeyA and PokeyB in rDNA and the rest of the genome suggest these elements have low transposition rates, high deletion rates, and/or strong purifying selection against them at the host level. Further, PokeyA may have a higher transposition rate than PokeyB. In these species, mPok1 was not found, and mPok2 is likely inactive. In comparison, the fifth species, D. arenata, which may be a hybrid, has higher Pokey numbers. Higher Pokey numbers could be due to release from epigenetic repression following hybridization. / Ontario Graduate Scholarship in Science and Technology to Shannon H. C. Eagle, Natural Sciences and Engineering Research Council of Canada Discovery Grant to Dr. Teresa J. Crease

A high-resolution computer-based survey for transposable elements performed on 910 Kb of rice genomic DNA sequences revealed the presence of both class I and class II transposable elements. Elements from most major families of plant transposable elements were identified, and new groups were reported for these families. Miniature inverted-repeat transposable elements (MITES) are clearly the predominant type of transposable element in the rice sequences examined. Phylogenetic analysis of the putative transposases of several transposable elements indicated that Tourist-like miniature inverted-repeat transposable elements (MITES) are closely related to the bacterial insertion sequence 5 (IS5) family of transposable elements, while Emigrant-like and Stowaway-like MITES are both related to members of the IS630/TcI/mariner superfamily of elements. Finally, the nucleotide sequences of MITES, Ac-like, Mutator-like elements (MULE), short interspersed nuclear elements (SINEs) and other unclassified elements, as well as their insertion polymorphism data have been used to reconstruct the relationships between rice species in the AA genome. The use of a combination of transposable element data sets generated the most reliable cladograms.

Transcriptional fusion mutants and Tn5-B20 transposon mutants were isolated where the only genes affected are believed to either be involved in the hypothetical GABA shunt or code for subunits of the alpha-ketoglutarate dehydrogenase enzyme complex of Sinorhizobium meliloti. The growth phenotypes of Rm30222 (gabT) and eight mutants in gabD1, 2, 3, and 4 on minimal media were comparable to that of the wild-type. Compared to wild-type, Rm30222 (gabT) lacked alpha-ketoglutarate-dependent gamma-aminobutyrate transaminase activity showed high induction of gabT on GABA but produced green plants indicative of being Fix+. Mutants in gabD alleles maintained wild-type levels of succinic semialdehyde dehydrogenase activity and could fix nitrogen as well as the wild-type in symbiosis. / Mutation of sucB encoding a subunit of a-ketoglutarate dehydrogenase produced a mutant, Rm30230, that initially had difficulty growing on minimal media supplemented with either arabinose or glutamate. In symbiosis with alfalfa, Rm30230 had a fix- phenotype and was also devoid of alpha-ketoglutarate dehydrogenase activity. The ability of Rm30230 to grow on arabinose or glutamate, without alpha-ketoglutarate dehydrogenase activity, strengthens the hypothesis that S. meliloti has a functional GABA shunt allowing it to circumvent the forward-direction TCA cycle from alpha-ketoglutarate to succinate. Mutation of the second potential dihydrolipoamide succinyltransferase component (E2) of alpha-ketoglutarate dehydrogenase yielded Rm30267 (SMb20019) with wild-type growth on minimal media and a Fix+ phenotype in plants. The introduction or a sucB mutation into the SMb20019 mutant background (Rm30275) was comparable to the sole sucB mutation. This finding shows that the locus SMb20019 cannot be substituted for sucB in the alpha-ketoglutarate dehydrogenase enzyme complex.

The population dynamics of transposons in self- and cross-fertilizing plant populations are investigated both theoretically and empirically. Models were developed to evaluate the influence of host breeding system on transposon populations. Modeling results suggest that the selfing rate is likely to have important effects on the abundance and polymorphism patterns of transposable elements in plant genomes. A primary characterization of diversity and abundance of transposons in the self-pollinating species Arabidopsis thaliana was conducted using genomic sequencing data, providing strong evidence for recent element mobility. Utilizing this information, a PCR-based approach was implemented to examine transposon dynamics in populations of Arabidopsis thaliana and its outcrossing relative, Arabidopsis lyrata. The results provide evidence for the importance of purifying selection in controlling transposon abundance in outcrossing populations, but not in selfers. Differences observed between the species are consistent with the hypothesis that host breeding systems influence the selective pressure acting on transposons.

Transposons are mobile genetic elements that have the potential to cause mutations as a result of different aspects of their life cycle. Because most of these mutations are detrimental and due to a selfish life cycle seemingly aiming at increasing their numbers, transposons have been regarded as "junk" DNA that contributes no evolutionary function to the host organism. In this thesis, I argue that although most of the transposon-induced mutations are detrimental, some may lead to benefits for the host and become adaptive. I discuss recent evidence from the literature that points to several mechanisms by which transposons and transposon activity may lead to the diversification of host genes and gene functions. I also provide evidence that transposons have inserted in the 5' flanking region of the gene coding for maize and teosinte auxin-binding protein 1 (Abp1). These transposons do not change the structure of the Abp1 transcripts but may modulate Abp1 gene expression quantitatively. In addition, I document the first case outside of oncogenic retroviruses, of a retrotransposon (called Bs1) that transduced portions from three different maize genes. I show that the Bs1-associated transduction events resulted in the formation of one uninterrupted open reading frame that is both transcribed and translated in reproductive tissues. I suggest that, such as in the case of Bs1, gene transduction by retroelements may be a general mechanism for the evolution of new hybrid genes by the shuffling of host sequences. I conclude that transposons are better regarded as means for the generation of gene and genomic diversity. Natural selection will favor and fix adaptive variants whereas detrimental mutations are likely to be purged out of the population.

Thesis (Ph.D.)--Biology, Georgia Institute of Technology, 2008. / Committee Chair: Jordan, I. King; Committee Member: Borodovsky, Mark; Committee Member: Bunimovich, Leonid; Committee Member: Choi, Jung; Committee Member: McDonald, John.

Thesis (M.A.)--York University, 2007. Graduate Programme in Biology. / Typescript. Includes bibliographical references (leaves 53-63). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR31999

While the study of transposable element evolution has been conducted in several model insect organisms such as Anopheles gambiae, Drosophila melanogaster, and Bombyx mori, little investigation has been conducted into the transposable element (TE) evolution within less commonly examined model and non-model taxa within Diptera. In this work we contributed two analyses to close this gap. First, TEs in the lepidopteran, Heliconius melpomene, were characterized, and it was determined that 25% of the genome is composed of TEs. Second, TEs in oestroid and muscid flies were characterized using survey sequencing rather than whole genomes. Comparative analyses were performed on Haematobia irritans, Sarcophaga crassipalpis, Phormia regina, and Cochliomyia hominivorax. TE proportions were 5.95%, 10.00%, 22.43%, and 30.67%, for C. hominivorax, P. regina, S. crassipalpis and H. irritans, respectively. These studies provide new insights into the diversity of TEs in Insecta and suggest that in general, TE diversity is high among insects.