subject:(Transposable elements)

University of Rochester

1. Vedanayagam, Jeffrey P. Evolutionary genomics of piRNA mediated transposon silencing in Drosophila.

Degree: PhD, 2016, University of Rochester

► Transposable elements (TEs) are abundant throughout the genomes of most living organisms. A recently identified piwi-interacting RNA (piRNA) pathway has been shown to defend against… (more)

▼ Transposable elements (TEs) are abundant throughout the genomes of most living organisms. A recently identified piwi-interacting RNA (piRNA) pathway has been shown to defend against TEs in the Drosophila germline. This dissertation research is an evolutionary genomic analysis of the piRNA pathway in closely related Drosophila species. In Chapter 1, we characterize the rate of evolution for proteins affecting 26 RNAi knockdown phenotypes, which include three phenotypes related to regulation of transposon integration. When RNAi phenotypes are grouped into categories according to cellular function, we find that genes involved in the greatest number of phenotypic categories are also significantly more likely to have a history of rapid protein evolution. Defining pleiotropy using phenotypic categories yields different results than studies that define pleiotropy based on physical interactions. In Chapter 2, we characterize the expression diversity of several families of TEs using piRNAs. Comparative genomic analysis of piRNA expression finds dynamic changes in expression levels of several families of TEs in D. melanogaster and the D. simulans clade. Measuring ping-pong activity— a signature of piRNA amplification finds higher mean piRNA amplification in D. simulans and D. mauritiana, suggesting increased activity of several TEs in these species compared to D. melanogaster. Furthermore, McDonald-Kreitman tests identify three genes in the piRNA pathway as having experienced recent positive selection in D. simulans, and one gene each in D. melanogaster and D. mauritiana. All four genes are components of nuage, which is a macromolecular complex that mediate protein-protein and protein-RNA interactions. Our results are consistent with a model of antagonistic co-evolution between TEs and the piRNA pathway. In Chapter 3, we use single-molecule sequencing to perform a detailed comparative analysis of the flamenco piRNA cluster in both D. melanogaster and D. mauritiana. Our analysis reveals that there is very little sequence homology of flamenco between the two species, indicating rapid turnover of TE sequence. Furthermore, spatial heterogeneity in piRNA abundance in the flamenco region identifies two putative piRNA clusters adjacent to flamenco that may be functionally distinct. This study is the first practical demonstration of re-constructing the genome sequence of highly repetitive piRNA clusters in closely related Drosophila species.

Subjects/Keywords: Drosophila; piRNA; Transposable elements

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APA (6^th Edition):

Vedanayagam, J. P. (2016). Evolutionary genomics of piRNA mediated transposon silencing in Drosophila. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/30638

Chicago Manual of Style (16^th Edition):

Vedanayagam, Jeffrey P. “Evolutionary genomics of piRNA mediated transposon silencing in Drosophila.” 2016. Doctoral Dissertation, University of Rochester. Accessed January 16, 2021. http://hdl.handle.net/1802/30638.

MLA Handbook (7^th Edition):

Vedanayagam, Jeffrey P. “Evolutionary genomics of piRNA mediated transposon silencing in Drosophila.” 2016. Web. 16 Jan 2021.

Vancouver:

Vedanayagam JP. Evolutionary genomics of piRNA mediated transposon silencing in Drosophila. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1802/30638.

Council of Science Editors:

Vedanayagam JP. Evolutionary genomics of piRNA mediated transposon silencing in Drosophila. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/30638

University of Michigan

2. Flasch, Diane. LINE-1 Integration Preferences in Human Somatic Cells.

Degree: PhD, Human Genetics, 2017, University of Michigan

URL: http://hdl.handle.net/2027.42/140966

► Long INterspersed Element-1 (LINE-1 or L1) is the only autonomously active transposable element in the human genome. The vast majority of L1s are inactive, but… (more)

▼ Long INterspersed Element-1 (LINE-1 or L1) is the only autonomously active transposable element in the human genome. The vast majority of L1s are inactive, but a small number (~80-100 per human genome) retain the ability to mobilize by a ‘copy and paste’ mechanism called retrotransposition. L1 encodes two proteins (ORF1p and ORF2p) required for retrotransposition. ORF2p is a 150kDa protein that has endonuclease (EN) and reverse transcriptase (RT) activities that are responsible for initiating L1 integration by a mechanism termed target-site primed reverse transcription (TPRT). During canonical TPRT, the L1 EN makes a single-strand endonucleolytic nick at a double-stranded genomic DNA target sequence (typically 5’-TTTT/A-3’ and variants of that sequence), to expose a 3’-hydroxyl group that is used as a primer by the L1 RT to reverse transcribe L1 messenger RNA. Different types of transposable elements (TEs) have evolved convergent strategies to target genomic ‘safe havens,’ where TE insertions are predicted to have relatively minimal effects on host fitness and gene expression. Whether L1 integrates into specific genomic regions requires elucidation. In this thesis, I have examined L1 integration preferences in four human cell lines that are proxies for in vivo cell types known to accommodate endogenous de novo L1 retrotransposition events. By combining cultured cell, molecular biological, the Pacific Bioscience sequencing platform, and computational approaches, I characterized 65,079 de novo engineered human L1 integration sites. I compared our L1 insertion dataset to a weighted random model, which assumes that L1 integration preferences are mediated solely by the presence of a degenerate L1 EN consensus cleavage site in the human genome. The data suggest that gene content, transcriptional activity, strand bias, epigenetic environment, and DNA replication status have minimal effects on L1 integration. Thus, L1 EN is the principal determinant of L1 integration. In contrast to canonical EN-dependent L1 retrotransposition, previous studies indicated that L1s could also integrate at sites of DNA damage, including dysfunctional telomeres, by an endonuclease-independent (ENi) mechanism in certain cultured cell lines that contain mutations in genes that render the non-homologous end-joining (NHEJ) pathway of DNA repair and p53 inactive. Here, we explored whether the disruption of other DNA repair pathways influence ENi L1 integration. We observed ENi retrotransposition in certain tissue culture cell lines containing defects in the Fanconi anemia (FA) DNA repair pathway. Since defects in the FA pathway can lead to the accumulation of inter-strand DNA crosslinks that, if left unrepaired, can interfere with DNA replication, we hypothesized that lesions arising at stalled DNA replication forks may provide substrates for enhanced ENi retrotransposition. Indeed, the examination of L1 EN mutant integration sites in FANCD2-deficient cells, suggests that a 3’-hydroxyl group present at Okazaki fragments and/or double-strand DNA… Advisors/Committee Members: Moran, John V (committee member), Wilson, Thomas E (committee member), Boehnke, Michael Lee (committee member), Kidd, Jeffrey (committee member), Mills, Ryan Edward (committee member), Rothman, Edward D (committee member).

Subjects/Keywords: Transposable Elements; Genetics; Science

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Flasch, D. (2017). LINE-1 Integration Preferences in Human Somatic Cells. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/140966

Chicago Manual of Style (16^th Edition):

Flasch, Diane. “LINE-1 Integration Preferences in Human Somatic Cells.” 2017. Doctoral Dissertation, University of Michigan. Accessed January 16, 2021. http://hdl.handle.net/2027.42/140966.

MLA Handbook (7^th Edition):

Flasch, Diane. “LINE-1 Integration Preferences in Human Somatic Cells.” 2017. Web. 16 Jan 2021.

Vancouver:

Flasch D. LINE-1 Integration Preferences in Human Somatic Cells. [Internet] [Doctoral dissertation]. University of Michigan; 2017. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/2027.42/140966.

Council of Science Editors:

Flasch D. LINE-1 Integration Preferences in Human Somatic Cells. [Doctoral Dissertation]. University of Michigan; 2017. Available from: http://hdl.handle.net/2027.42/140966

3. Charles, Mathieu. Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation.

Degree: Docteur es, Bioinformatique, 2010, Evry-Val d'Essonne

URL: http://www.theses.fr/2009EVRY0023

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Ma thèse vise à caractériser l’évolution dynamique et l’organisation des génomes des différentes espèces du blé (genres Triticum et Aegilops) en relation avec la prolifération… (more)

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Ma thèse vise à caractériser l’évolution dynamique et l’organisation des génomes des différentes espèces du blé (genres Triticum et Aegilops) en relation avec la prolifération des éléments transposables (TEs) dans leur génome (>80%), les polyploïdisations récurrentes ainsi que la syntenie avec d’autres espèces de la famille des Poaceae. En constituant des sets de séquences génomiques représentatives et en étudiant la variabilité entre des haplotypes des génomes du blé, j’ai caractérisé la dynamique et la prolifération différentielle des TEs qui est la résultante de l’équilibre entre leurs insertions et aussi leurs éliminations actives. Le taux moyen de remplacement de l’espace TEs, mesurant les différences de séquences dues aux insertions et aux délétions entre deux haplotypes, a été ainsi estimé à 86% par million d’années (Ma) et dépasse celles bien documentées du maïs. Les insertions des TEs mais aussi leurs éliminations par recombinaisons illégitimes de l’ADN (pouvant atteindre plusieurs dizaines de kb) ainsi que les recombinaisons génétiques entre haplotypes divergents représentent les principaux mécanismes à la base des changements rapides de l’espace TEs. Sur une échelle d’évolution plus longue (60 Ma), j’ai analysé la conservation des gènes et l’évolution du locus (Ha) entre différentes espèces des Poaceae. J’ai pu ainsi préciser l’émergence du caractère grain tendre et des gènes Ha, comme nouveaux membres de la famille des gènes de Prolamine, dans l’ancêtre commun des Pooideae (blé et Brachypodium, de la tribu des Triticeae et des Brachypodieae) et des Ehrhartoideae (riz), après leur divergence des Panicoideae (maïs, sorgho).

My PhD aims to characterize dynamic evolution and organization of wheat genomes from différent species (Triticum and Aegilops genera) in relation to transposable element (TE) proliferation in their genomes (>80%), polyploidizations and synteny with other Poaceae species. By constituting and comparing representative genomic sequences and analyzing haplotype variability of the wheat genomes, I have characterized dynamics and differential proliferation of TEs, as resulting from the combinations of their insertions and deletions. Mean replacement rate of the TE space, which measures sequence differences due to insertion and removal of TEs between two haplotypes, was estimated to 86% per one million year (My). This is more important than the well-documented haplotype variability found in maize. It was observed that TE insertions and DNA elimination by illegitimate recombination (implicating several ‘tens’ of kb) as well as homologous recombination between divergent haplotypes represent the main molecular basis for rapid change of the TE space. At a longer evolutionary scale (60 My), I have compared gene conservation at the Ha locus region between different Poaceae species. The comparative genome analysis and evolutionary comparison with genes encoding grain reserve proteins of grasses suggest that an ancestral Ha-like gene emerged, as a new member of the Prolamin gene family, in a common…

Advisors/Committee Members: Chalhoub, Boulos (thesis director).

Subjects/Keywords: Éléments transposables; Transposable elements

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APA (6^th Edition):

Charles, M. (2010). Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation. (Doctoral Dissertation). Evry-Val d'Essonne. Retrieved from http://www.theses.fr/2009EVRY0023

Chicago Manual of Style (16^th Edition):

Charles, Mathieu. “Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation.” 2010. Doctoral Dissertation, Evry-Val d'Essonne. Accessed January 16, 2021. http://www.theses.fr/2009EVRY0023.

MLA Handbook (7^th Edition):

Charles, Mathieu. “Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation.” 2010. Web. 16 Jan 2021.

Vancouver:

Charles M. Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation. [Internet] [Doctoral dissertation]. Evry-Val d'Essonne; 2010. [cited 2021 Jan 16]. Available from: http://www.theses.fr/2009EVRY0023.

Council of Science Editors:

Charles M. Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes : Wheat (Aegilops and Triticum genera) genome evolution within the Poaceae : rapid dynamic of the space occupied by transposable elements and relative gene conservation. [Doctoral Dissertation]. Evry-Val d'Essonne; 2010. Available from: http://www.theses.fr/2009EVRY0023

Rochester Institute of Technology

4. Rosato, Andrew J. Regulation of Transposable Elements by Tumor Suppressor Protein 53.

Degree: MS, Thomas H. Gosnell School of Life Sciences (COS), 2020, Rochester Institute of Technology

URL: https://scholarworks.rit.edu/theses/10626

► Multiple transposable elements have been identified by colocalization analysis that display a strong predicted regulatory relationship with p53 associated peaks. RNA-Seq was used to… (more)

Subjects/Keywords: Colocalization; TP53; Transposable elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rosato, A. J. (2020). Regulation of Transposable Elements by Tumor Suppressor Protein 53. (Masters Thesis). Rochester Institute of Technology. Retrieved from https://scholarworks.rit.edu/theses/10626

Chicago Manual of Style (16^th Edition):

Rosato, Andrew J. “Regulation of Transposable Elements by Tumor Suppressor Protein 53.” 2020. Masters Thesis, Rochester Institute of Technology. Accessed January 16, 2021. https://scholarworks.rit.edu/theses/10626.

MLA Handbook (7^th Edition):

Rosato, Andrew J. “Regulation of Transposable Elements by Tumor Suppressor Protein 53.” 2020. Web. 16 Jan 2021.

Vancouver:

Rosato AJ. Regulation of Transposable Elements by Tumor Suppressor Protein 53. [Internet] [Masters thesis]. Rochester Institute of Technology; 2020. [cited 2021 Jan 16]. Available from: https://scholarworks.rit.edu/theses/10626.

Council of Science Editors:

Rosato AJ. Regulation of Transposable Elements by Tumor Suppressor Protein 53. [Masters Thesis]. Rochester Institute of Technology; 2020. Available from: https://scholarworks.rit.edu/theses/10626

5. Gutierrez Carnelossi, Elias Alberto. Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos.

Degree: Docteur es, Génétique et génomique évolutive, 2014, Université Claude Bernard – Lyon I

URL: http://www.theses.fr/2014LYO10036

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Les éléments transposable (Ets) ont un rôle important dans l’évolution, puisque ce sont des séquences d’ADN qui ont la capacité de se déplacer dans le… (more)

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Les éléments transposable (Ets) ont un rôle important dans l’évolution, puisque ce sont des séquences d’ADN qui ont la capacité de se déplacer dans le génome hôte. Nous cherchons à comprendre l’activité dans les croisements entre la Drosophile mojavensis et D. arizonae. La thèse est divisée en quatre chapitres, le première présente une analyse détaillée d'un rétrotransposon non-LTR appelé I , connu pour causer dysgénésie hybride D. melanogaster. Les analyses phylogénétiques réalisés, ont montré que les séquences I chez D. mojavensis et nourri par ceux d'autres espèces de Drosophila appartiennent, à des familles différentes d’ET. Les analyses d'expression par RTQ-PCR, a montré que cet élément est une activité de transcription dans les ovaires et les testicules des deux espèces et leurs hybrides, et ont une grande expression dans les testicules mais pas dans les ovaires des hybrides, qui pourraient être associés avec le mâle hybride phénotype de stérilité. Dans le deuxième chapitre sont présentées les analyses de TE exprimés dans les ovaires des deux souches parentales et leurs hybrides par l'ARN-Seq. Les résultats montrent des espèces spécifiques expression de TE chez les parents et les hybrides et d'une manière sans précédent, ET sont généralement réglementés en ce qui concerne les hybrides avec leurs parents, bien que certains d'entre eux sont surexprimés. Dans le troisième chapitre sont présentés les résultats de l'expression de quatre rétrotransposons (Helena, I, Copia et Osvaldo) quantifiés par RTQ -PCR; et enfin, dans le dernier chapitre, nous avons présenté des estimations de la taille du génome (C-valeur) dans les deux espèces parentales et hybrides réciproques. Dans l'ensemble, cette thèse révèle un scénario d'expression de TE spécifiques D. mojavensis et D. arizonae, et de sa réglementation dans les hybrides de rares exceptions près, qui peut nous aider à comprendre la complexité de la dynamique et de l'action de ces éléments mobiles dans la spéciation procédé de différentes espèces

The transposable elements (TEs) have an important role in evolution, since they are DNA sequences that have the ability to move into the host genome. We seek to understand the activity of the TEs in crosses between Drosophila mojavensis and D. arizonae. The thesis is divided into four chapters. The first presents a detailed analysis of an non- LTR retrotransposon called I, known to cause hybrid dysgenesis in D. melanogaster. Putatively active sequences similar to the I element were identified and characterized in the genome of D. mojavensis. The performed phylogenetic analyzes showed that the I sequences in D. mojavensis and those harbored by other Drosophila species belong to different I families. Expression analyses by RTq-PCR showed that this element is transcriptionally active in ovaries and testes of both species and their hybrids, and have high expression in the testes, but not in the hybrids ovaries, which could be associated with the male hybrid sterility phenotype. In the second chapter are presented analyses of…

Advisors/Committee Members: Vieira-Heddi, Cristina (thesis director), Carareto, Claudia marcia aparecida (thesis director).

Subjects/Keywords: Éléments transposable; Hybrides; Drosophila; Retrotransposon; Transposable elements; Hybrids; Drosophila; Retrotransposon; 572.38

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gutierrez Carnelossi, E. A. (2014). Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos. (Doctoral Dissertation). Université Claude Bernard – Lyon I. Retrieved from http://www.theses.fr/2014LYO10036

Chicago Manual of Style (16^th Edition):

Gutierrez Carnelossi, Elias Alberto. “Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos.” 2014. Doctoral Dissertation, Université Claude Bernard – Lyon I. Accessed January 16, 2021. http://www.theses.fr/2014LYO10036.

MLA Handbook (7^th Edition):

Gutierrez Carnelossi, Elias Alberto. “Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos.” 2014. Web. 16 Jan 2021.

Vancouver:

Gutierrez Carnelossi EA. Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos. [Internet] [Doctoral dissertation]. Université Claude Bernard – Lyon I; 2014. [cited 2021 Jan 16]. Available from: http://www.theses.fr/2014LYO10036.

Council of Science Editors:

Gutierrez Carnelossi EA. Activité d'éléments transposables dans les populations de Drosophila mojavensis et D. arizonae et chez leurs hybrides : Investigação de elementos de transposição em populações de Drosophila mojavensis e D. arizonae e seus híbridos. [Doctoral Dissertation]. Université Claude Bernard – Lyon I; 2014. Available from: http://www.theses.fr/2014LYO10036

Universiteit Utrecht

6. Ravesteyn, T.W. van. The role of Transposable Elements in the Human Genome and their contribution to Evolution.

Degree: 2013, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/278058

► Transposable elements (TEs) were originally discovered in Zea mays in the 1950s by Barbara McClintock (MCCLINTOCK 1956). In essence, they are genetic elements that are… (more)

▼ Transposable elements (TEs) were originally discovered in Zea mays in the 1950s by Barbara McClintock (MCCLINTOCK 1956). In essence, they are genetic elements that are mobile and can move from one position to another within genomes. This concept fundamentally changed the view on genomes. Instead of rather static entities, it suggested that genomes are actually highly dynamic (Georgiev 1984). The draft of the human genome revealed that nearly half of the human genome is derived from transposable elements (Jurka et al. 2005; Lander et al. 2001). Britten and Davidson hypothesized that repetitive elements can act to distribute regulatory sequences throughout the genome, and thereby enriching, possibly even creating, whole pathways (Britten and Davidson 1971). The adoption of a TE to a new function by the genome is called “exaptation” (Gould and Vrba 1982), and would enhance genetic innovation. In this sense, they can be viewed as catalysts of evolution because their contribution to variation might have increased the speed of evolution on the human lineage (Britten 2010). Here, I will present an overview of the role of TEs in the human genome and their suggested influences on human evolution. In summary, it is obvious that TEs are really an integrated part of our genomes. It seems that the reduction of effective population size during evolution enabled the accumulation of TEs in most of the eukaryotic organisms. TEs provided the necessary base pairs which were needed to generate new genes and to acquire regulatory functions. They had probably the most profound influences on genome architecture in the early times of evolution and during moments of rapid population expansions. During following evolutionary periods TE derived fragments may have evolved slowly into functional elementsIn addition to effects caused by direct insertion, it seems that TEs had a profound impact on genome evolution by recombination events. The immense TE copy number within the human genome increases the chance of recombination events which can lead to structural variation such as genome duplications, deletions and inversions. Thus, TEs may also affect genome structure after insertion by TE mediated recombination events. It seems difficult to find TEs that can be really related to recent human evolution, the identification of recent integrations might learn us more about the mechanism of transposition, evolutionary selection in the human lineage and the current effect of TE activity on human health. Advisors/Committee Members: Kovel, C.G.F de, Snel, B..

Subjects/Keywords: Transposable elements; TE; retroelements; human genome; evolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ravesteyn, T. W. v. (2013). The role of Transposable Elements in the Human Genome and their contribution to Evolution. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/278058

Chicago Manual of Style (16^th Edition):

Ravesteyn, T W van. “The role of Transposable Elements in the Human Genome and their contribution to Evolution.” 2013. Masters Thesis, Universiteit Utrecht. Accessed January 16, 2021. http://dspace.library.uu.nl:8080/handle/1874/278058.

MLA Handbook (7^th Edition):

Ravesteyn, T W van. “The role of Transposable Elements in the Human Genome and their contribution to Evolution.” 2013. Web. 16 Jan 2021.

Vancouver:

Ravesteyn TWv. The role of Transposable Elements in the Human Genome and their contribution to Evolution. [Internet] [Masters thesis]. Universiteit Utrecht; 2013. [cited 2021 Jan 16]. Available from: http://dspace.library.uu.nl:8080/handle/1874/278058.

Council of Science Editors:

Ravesteyn TWv. The role of Transposable Elements in the Human Genome and their contribution to Evolution. [Masters Thesis]. Universiteit Utrecht; 2013. Available from: http://dspace.library.uu.nl:8080/handle/1874/278058

Mississippi State University

7. Platt, Roy Nelson. Using transposable elements as tools to better understand evolution at the genomic level.

Degree: PhD, Biochemistry, Molecular Biology, Entomology and Plant Pathology, 2014, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03042014-101102/ ;

► Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not… (more)

▼ Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not uncommon for 50% of the genome to be derived from TEs, yet they remain an underutilized tool for tracking evolutionary change. With the increasing number of publicly funded genome projects and affordable access to next-generation sequencing platforms, it is important to demonstrate the role TEs may play in helping us understand evolutionary patterns. The research presented herein utilizes TEs to investigate such patterns at the genomic, specific, and generic levels in three distinct ways. First at the genomic level, an analysis of the historical TE activity within the thirteen-lined ground squirrel (Spermophilus tridecemlineatus) shows that non-LTR retrotransposon activity has been declining for the past ~26 million years and appears to have ceased ~5 million years ago. Since most mammals, and all other rodents studied to date, have active TEs the extinction event in S. tridecemlineatus makes it a valuable model for understanding the factors driving TE activity and extinction. Second, we examined TEs as factors impacting genomic and species diversity. We found that DNA transposon insertions in Eptesicus fuscus, appear to have been exapted as miRNAs. When placed within a phylogenetic context a burst of transposon-driven, miRNA origination and the vespertilionid species radiation occurred simultaneously ~30 million years ago. This observation implies that lineage specific TEs could generate lineage specific regulatory pathways, and consequently lineage specific phenotypic differences. Finally, we utilized TEs to investigate their phylogenetic potential at the level of genus. In particular a method was developed that identified, over 670 thousand Ves SINE insertions in seven species of Myotis for use in future phylogenetic studies. Our method was able to accurately identify insertions in taxa for which no reference genome was available and was confirmed using traditional PCR and Sanger sequencing methods. By identifying polymorphic Ves insertions, it may be possible to resolve the phylogeny of one of the largest species radiations in mammals. Advisors/Committee Members: Federico G. Hoffmann (chair), David A. Ray (chair), Daniel Peterson (committee member), Richard D. Stevens (committee member), Andy D. Perkins (committee member).

Subjects/Keywords: retrotransposons; DNA transposons; transposable elements; genome evolution

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APA (6^th Edition):

Platt, R. N. (2014). Using transposable elements as tools to better understand evolution at the genomic level. (Doctoral Dissertation). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-03042014-101102/ ;

Chicago Manual of Style (16^th Edition):

Platt, Roy Nelson. “Using transposable elements as tools to better understand evolution at the genomic level.” 2014. Doctoral Dissertation, Mississippi State University. Accessed January 16, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-03042014-101102/ ;.

MLA Handbook (7^th Edition):

Platt, Roy Nelson. “Using transposable elements as tools to better understand evolution at the genomic level.” 2014. Web. 16 Jan 2021.

Vancouver:

Platt RN. Using transposable elements as tools to better understand evolution at the genomic level. [Internet] [Doctoral dissertation]. Mississippi State University; 2014. [cited 2021 Jan 16]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03042014-101102/ ;.

Council of Science Editors:

Platt RN. Using transposable elements as tools to better understand evolution at the genomic level. [Doctoral Dissertation]. Mississippi State University; 2014. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03042014-101102/ ;

Mississippi State University

8. Lavoie, Christine A. Transposable element content in non-model insect genomes.

Degree: MS, Biochemistry, Molecular Biology, Entomology and Plant Pathology, 2014, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03112014-133706/ ;

► While the study of transposable element evolution has been conducted in several model insect organisms such as Anopheles gambiae, Drosophila melanogaster, and Bombyx mori,… (more)

Subjects/Keywords: transposable elements; transposons; lepidoptera; oestroid; muscid

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APA (6^th Edition):

Lavoie, C. A. (2014). Transposable element content in non-model insect genomes. (Masters Thesis). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-03112014-133706/ ;

Chicago Manual of Style (16^th Edition):

Lavoie, Christine A. “Transposable element content in non-model insect genomes.” 2014. Masters Thesis, Mississippi State University. Accessed January 16, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-03112014-133706/ ;.

MLA Handbook (7^th Edition):

Lavoie, Christine A. “Transposable element content in non-model insect genomes.” 2014. Web. 16 Jan 2021.

Vancouver:

Lavoie CA. Transposable element content in non-model insect genomes. [Internet] [Masters thesis]. Mississippi State University; 2014. [cited 2021 Jan 16]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03112014-133706/ ;.

Council of Science Editors:

Lavoie CA. Transposable element content in non-model insect genomes. [Masters Thesis]. Mississippi State University; 2014. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03112014-133706/ ;

9. Jin, Lingling. Interruptional Activity and Simulation of Transposable Elements.

Degree: 2017, University of Saskatchewan

URL: http://hdl.handle.net/10388/8084

► Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. The active TEs along with the remnants… (more)

▼ Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. The active TEs along with the remnants of many transposition events over millions of years constitute 46.69% of the human genome. TEs are believed to promote speciation and their activities play a significant role in human disease. The 22 AluY and 6 AluS TE subfamilies have been the most active TEs in recent human history, whose transposition has been implicated in several inherited human diseases and in various forms of cancer by integrating into genes. Therefore, understanding the transposition activities is very important. Recently, there has been some work done to quantify the activity levels of active Alu transposable elements based on variation in the sequence. Here, given this activity data, an analysis of TE activity based on the position of mutations is conducted. Two different methods/simulations are created to computationally predict so-called harmful mutation regions in the consensus sequence of a TE; that is, mutations that occur in these regions decrease the transposition activities dramatically. The methods are applied to AluY, the youngest and most active Alu subfamily, to identify the harmful regions laying in its consensus, and verifications are presented using the activity of AluY elements and the secondary structure of the AluYa5 RNA, providing evidence that the method is successfully identifying harmful mutation regions. A supplementary simulation also shows that the identified harmful regions covering the AluYa5 RNA functional regions are not occurring by chance. Therefore, mutations within the harmful regions alter the mobile activity levels of active AluY elements. One of the methods is then applied to two additional TE families: the Alu family and L1 family, in detecting the harmful regions in these elements computationally. Understanding and predicting the evolution of these TEs is of interest in understanding their powerful evolutionary force in shaping their host genomes. In this thesis, a formal model of TE fragments and their interruptions is devised that provides definitions that are compatible with biological nomenclature, while still providing a suitable formal foundation for computational analysis. Essentially, this model is used for fixing terminology that was misleading in the literature, and it helps to describe further TE problems in a precise way. Indeed, later chapters include two other models built on top of this model: the sequential interruption model and the recursive interruption model, both used to analyze their activity throughout evolution. The sequential interruption model is defined between TEs that occur in a genomic sequence to estimate how often TEs interrupt other TEs, which has been shown to be useful in predicting their ages and their activity throughout evolution. Here, this prediction from the sequential interruptions is shown to be closely related to a classic matrix optimization problem: the Linear Ordering Problem (LOP). By… Advisors/Committee Members: Vassileva, Julita, Kusalik, Tony, McQuillan, Ian, Keil, Mark.

Subjects/Keywords: Transposable elements; transpositional activity; theoretical modelling

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APA (6^th Edition):

Jin, L. (2017). Interruptional Activity and Simulation of Transposable Elements. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/8084

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Jin, Lingling. “Interruptional Activity and Simulation of Transposable Elements.” 2017. Thesis, University of Saskatchewan. Accessed January 16, 2021. http://hdl.handle.net/10388/8084.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Jin, Lingling. “Interruptional Activity and Simulation of Transposable Elements.” 2017. Web. 16 Jan 2021.

Vancouver:

Jin L. Interruptional Activity and Simulation of Transposable Elements. [Internet] [Thesis]. University of Saskatchewan; 2017. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10388/8084.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Jin L. Interruptional Activity and Simulation of Transposable Elements. [Thesis]. University of Saskatchewan; 2017. Available from: http://hdl.handle.net/10388/8084

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queen Mary, University of London

10. Yeoh, Joseph Guan Chong. Artificial horizontal transfer of retroposons.

Degree: PhD, 2014, Queen Mary, University of London

URL: http://qmro.qmul.ac.uk/xmlui/handle/123456789/8972 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667349

► Many factors may explain why certain transposable elements (TEs) spread in some species and not others. On the one hand, they include processes that affect… (more)

▼ Many factors may explain why certain transposable elements (TEs) spread in some species and not others. On the one hand, they include processes that affect the rate of transposition, such as differences in the regulation of expression; on the other hand, they include characteristics of a genome that affect the consequences of transposition. In particular genome size may have an effect: a genome that is large due to non-essential repetitive DNA may be permissive for TE movement, as insertion events are less likely to be deleterious. Genome size may also help explain the pattern of TE distribution between species of mosquitoes, including the important vectors of arboviruses, Aedes aegypti and Culex pipiens sensu lato. These species have genomes 3- 5 times larger than a third genus, the Anopheles mosquitoes, which includes the malaria vectors. While all mosquitoes carry a diverse range of TEs, only culicines have the super abundant retroposon, Juan which can contribute up to 3% of the genome. The genome sequences of various insect species were compared and the mosquitoes show a significant trend of increase in genome size, which can be attributed to the increase in retroposon sequences. Two variants of Juan are reported, and new information is added regarding these elements. Previous publication of these elements contained errors in their sequences. A unique triple repeat of a cysteine rich region with a CCHC motif is present in the open reading frame. This sequence is a zinc-knuckle domain, important for the replication mechanism of these elements. In comparison, a third recently active but very low copy number retroposon, termed Pip1, is also described. The results show that Pip1 is related to the Juan elements and also possess the triple CCHC motif. The PCR results also supports previous findings of polymorphism in insertion sites of this element, suggesting that Pip1 was active after the establishment of the different strains. Pip1 copies can be grouped into three distinct groups based on nucleotide differences. Pip1 could also be using an alternative start codon to initiate transcription. Full length intact copies of the three TEs in this study were been cloned into a germline transformation vector based on piggyBac and used for germline transformation in Drosophila melanogaster. Drosophila melanogaster has no Juan or Pip1 elements and an even smaller genome than anophelines mosquitoes, so insertion events from unregulated TE movement should be more detectable. We found that the elements have been successfully introduced into the Drosophila lines. The lines were inbred to obtain a homozygous population. A range of transformed lines were monitored. No effects of hybrid dysgenesis was found. Flies with black spotted eyes were identified in a Pip1 line but this phenotype was not heritable. Whole genome sequencing was carried out on the flies using next generation sequencing (NGS) technology. Retroposon sequences was detected at a high frequency. Insertion junctions were not detected but this result does not eliminate…

Subjects/Keywords: 572.8; Biology; Insect genomes; Retroposons; Transposable elements

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APA (6^th Edition):

Yeoh, J. G. C. (2014). Artificial horizontal transfer of retroposons. (Doctoral Dissertation). Queen Mary, University of London. Retrieved from http://qmro.qmul.ac.uk/xmlui/handle/123456789/8972 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667349

Chicago Manual of Style (16^th Edition):

Yeoh, Joseph Guan Chong. “Artificial horizontal transfer of retroposons.” 2014. Doctoral Dissertation, Queen Mary, University of London. Accessed January 16, 2021. http://qmro.qmul.ac.uk/xmlui/handle/123456789/8972 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667349.

MLA Handbook (7^th Edition):

Yeoh, Joseph Guan Chong. “Artificial horizontal transfer of retroposons.” 2014. Web. 16 Jan 2021.

Vancouver:

Yeoh JGC. Artificial horizontal transfer of retroposons. [Internet] [Doctoral dissertation]. Queen Mary, University of London; 2014. [cited 2021 Jan 16]. Available from: http://qmro.qmul.ac.uk/xmlui/handle/123456789/8972 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667349.

Council of Science Editors:

Yeoh JGC. Artificial horizontal transfer of retroposons. [Doctoral Dissertation]. Queen Mary, University of London; 2014. Available from: http://qmro.qmul.ac.uk/xmlui/handle/123456789/8972 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667349

Brandeis University

11. Kanodia, Abhay. Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes.

Degree: 2016, Brandeis University

URL: http://hdl.handle.net/10192/31816

► Transposons are mobile genetic elements that make up a significant portion of metazoan genomes, such as ~12% of Drosophila melanogaster’s genome. Since active transposons can… (more)

Subjects/Keywords: D. melanogaster; TIDAL; Transposable Elements; genomic PCR

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APA (6^th Edition):

Kanodia, A. (2016). Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes. (Thesis). Brandeis University. Retrieved from http://hdl.handle.net/10192/31816

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kanodia, Abhay. “Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes.” 2016. Thesis, Brandeis University. Accessed January 16, 2021. http://hdl.handle.net/10192/31816.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kanodia, Abhay. “Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes.” 2016. Web. 16 Jan 2021.

Vancouver:

Kanodia A. Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes. [Internet] [Thesis]. Brandeis University; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10192/31816.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kanodia A. Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes. [Thesis]. Brandeis University; 2016. Available from: http://hdl.handle.net/10192/31816

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

12. Agren, Jon Arvid. Mating System Shifts and Transposable Element Evolution in Plants.

Degree: PhD, 2015, University of Toronto

URL: http://hdl.handle.net/1807/70840

► Transposable elements (TEs) are mobile genetic elements that can self-replicate and insert elsewhere in the genome. This movement often comes with a fitness cost and… (more)

▼ Transposable elements (TEs) are mobile genetic elements that can self-replicate and insert elsewhere in the genome. This movement often comes with a fitness cost and yet TEs are tremendously common. They contribute more than 80% to the largest plant genomes, but are much less abundant in the smallest plant genomes. Combined, these observations raise the two central questions of this thesis. First, why are TEs so common, and the genomes so large, in some species but not others? Second, what prevents TEs from completely taking over and causing genomes to fail to produce functional individual organisms? In this thesis, I have used population and comparative genomics approaches on whole genome data from closely related plant species and syntheisising literature reviews to examine some of the evolutionary causes and consequences of TE proliferation in plants. In particular, I have investigated the role of mating system shifts, from outcrossing to self-fertilization and from sexual to asexual reproduction, in driving variation in TE abundance and genome size. I used the reference genome of Capsella rubella as an outgroup to show that the higher TE abundance and larger genome size of the outcrossing Arabidopsis lyrata compared to selfing A. thaliana is due to TE driven expansion in the outcrosser rather than genome loss in the selfer. I investigated three Capsella species of contrasting mating system and found that the evolution of self-fertilization may have different effects on TE evolution on short and on long timescales. I applied a phylogenetic comparative approach and whole genome sequencing to demonstrate that sex and TEs cannot explain the variation in genome size in evening primroses (Oenothera). Using transcriptome data I showed that the chromosomal distribution (sex chromosomes vs. autosomes) of nuclear gene with organellar origin in Rumex hastatulus is not consistent with either co-adaptation or sexual conflict hypotheses. Finally, I showed that studying the proliferation of TEs offers insights to the cardinal problem of social evolution of what prevents selfish behaviour at lower levels from destroying functionality of the group. Overall, my thesis is a contribution to understanding the evolutionary causes and consequences of TE proliferation. Advisors/Committee Members: Wright, Stephen I, Ecology and Evolutionary Biology.

Subjects/Keywords: Genome size; Mating system; Transposable elements; 0412

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APA (6^th Edition):

Agren, J. A. (2015). Mating System Shifts and Transposable Element Evolution in Plants. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/70840

Chicago Manual of Style (16^th Edition):

Agren, Jon Arvid. “Mating System Shifts and Transposable Element Evolution in Plants.” 2015. Doctoral Dissertation, University of Toronto. Accessed January 16, 2021. http://hdl.handle.net/1807/70840.

MLA Handbook (7^th Edition):

Agren, Jon Arvid. “Mating System Shifts and Transposable Element Evolution in Plants.” 2015. Web. 16 Jan 2021.

Vancouver:

Agren JA. Mating System Shifts and Transposable Element Evolution in Plants. [Internet] [Doctoral dissertation]. University of Toronto; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1807/70840.

Council of Science Editors:

Agren JA. Mating System Shifts and Transposable Element Evolution in Plants. [Doctoral Dissertation]. University of Toronto; 2015. Available from: http://hdl.handle.net/1807/70840

13. Tetreault, Hannah M. Transposable element contribution and biological consequence of genome size variation among wild sunflower species.

Degree: PhD, Division of Biology, 2016, Kansas State University

URL: http://hdl.handle.net/2097/32897

► Nuclear genome size varies immensely across flowering plants, spanning nearly 2400-fold. The causes and consequences of this vast amount of variation have intrigued biologists since… (more)

▼ Nuclear genome size varies immensely across flowering plants, spanning nearly 2400-fold. The causes and consequences of this vast amount of variation have intrigued biologists since it became clear that nuclear DNA amount did not reflect organismal complexity (the so-called C-value paradox). In my dissertation I utilize wild sunflower species in the genus Helianthus to examine the role of transposable elements (TEs), and in particular, long terminal repeat (LTR) retrotransposons, in generating genome size variation and whether variation in genome size influences aspects of plant growth and development across multiple organizational levels. The genus Helianthus provides an excellent system for studying these questions given four-fold variation in nuclear DNA content among diploid species and well-resolved phylogenetic relationships. Utilizing short-read Illumina data and sequence information from a diverse panel of Helianthus annuus (common sunflower) full-length LTR retrotransposons, I found that nuclear genome size in Helianthus species is positively correlated with repetitive DNA, and LTR retrotransposon subtypes generally show similar patterns in genomic abundance across taxa. Helianthus species with the largest genomes, however, exhibit large-scale amplification of a small number of LTR retrotransposon subtypes. Measuring aspects of plant growth and development at cell-, organ- and whole plant-levels in a panel of diploid Helianthus species that vary 4-fold in nuclear genome size, I found that genome size is negatively correlated with cell production rate, but that this negative correlation does not persist at higher organizational levels. Taken together, these results provide insights into the mechanisms contributing to genome size evolution in plants and the organizational level at which genome size may impact growth patterns and developmental rates. Genome expansion in wild sunflowers is influenced most significantly by amplification of a small number of TEs and not necessarily by a greater diversity of TEs. Genome size is strongly negatively correlated with cell production rate but this relationship weakens at higher organizational levels, such as that of organ and whole-plant development. Advisors/Committee Members: Mark C. Ungerer.

Subjects/Keywords: Helianthus; Genome size; Transposable elements; Sunflowers

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APA (6^th Edition):

Tetreault, H. M. (2016). Transposable element contribution and biological consequence of genome size variation among wild sunflower species. (Doctoral Dissertation). Kansas State University. Retrieved from http://hdl.handle.net/2097/32897

Chicago Manual of Style (16^th Edition):

Tetreault, Hannah M. “Transposable element contribution and biological consequence of genome size variation among wild sunflower species.” 2016. Doctoral Dissertation, Kansas State University. Accessed January 16, 2021. http://hdl.handle.net/2097/32897.

MLA Handbook (7^th Edition):

Tetreault, Hannah M. “Transposable element contribution and biological consequence of genome size variation among wild sunflower species.” 2016. Web. 16 Jan 2021.

Vancouver:

Tetreault HM. Transposable element contribution and biological consequence of genome size variation among wild sunflower species. [Internet] [Doctoral dissertation]. Kansas State University; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/2097/32897.

Council of Science Editors:

Tetreault HM. Transposable element contribution and biological consequence of genome size variation among wild sunflower species. [Doctoral Dissertation]. Kansas State University; 2016. Available from: http://hdl.handle.net/2097/32897

University of Georgia

14. Chen, Tianle. DNA methylation analysis of the rice transposable elements mPing and Ping.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/24851

► Transposable elements are widely distributed in eukaryotes where they usually comprise the largest fraction of the genome. The Tourist-like MITE mPing was the first active… (more)

Subjects/Keywords: Transposable elements; MITE; rice; transposition; DNA methylation

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APA (6^th Edition):

Chen, T. (2014). DNA methylation analysis of the rice transposable elements mPing and Ping. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/24851

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chen, Tianle. “DNA methylation analysis of the rice transposable elements mPing and Ping.” 2014. Thesis, University of Georgia. Accessed January 16, 2021. http://hdl.handle.net/10724/24851.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chen, Tianle. “DNA methylation analysis of the rice transposable elements mPing and Ping.” 2014. Web. 16 Jan 2021.

Vancouver:

Chen T. DNA methylation analysis of the rice transposable elements mPing and Ping. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10724/24851.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chen T. DNA methylation analysis of the rice transposable elements mPing and Ping. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/24851

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

15. Sebastian, Bram. Computational prediction of miRNA precursors and miRNA targets.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/27002

► MicroRNA is small 22 nucleotides long non-coding RNA which regulates genes by targeting mRNA especially the 3’ UTR region. Identification of miRNAs and their targets… (more)

Subjects/Keywords: miRNA; miRNA targets; platypus; human; transposable elements

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APA (6^th Edition):

Sebastian, B. (2014). Computational prediction of miRNA precursors and miRNA targets. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/27002

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sebastian, Bram. “Computational prediction of miRNA precursors and miRNA targets.” 2014. Thesis, University of Georgia. Accessed January 16, 2021. http://hdl.handle.net/10724/27002.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sebastian, Bram. “Computational prediction of miRNA precursors and miRNA targets.” 2014. Web. 16 Jan 2021.

Vancouver:

Sebastian B. Computational prediction of miRNA precursors and miRNA targets. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10724/27002.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sebastian B. Computational prediction of miRNA precursors and miRNA targets. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/27002

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

16. Ellis, Nathanael Andrew. Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize.

Degree: 2016, University of Georgia

URL: http://hdl.handle.net/10724/34181

► The primary constriction site on a chromosome is called a centromere and is necessary for the faithful segregation of DNA during cell division. In maize,… (more)

▼ The primary constriction site on a chromosome is called a centromere and is necessary for the faithful segregation of DNA during cell division. In maize, centromeres are primarily made up of the class I transposable elements (TEs), CRM2 and tandem repeat, CentC. These repetitive sequences interact with the centromere defining histone variant, CENH3. In this study, transposon display (TD) was carried out to amplify CRM2 junction sites, creating 40 unique markers that are specific to the B centromere. CRM2-TD markers were genetically mapped to the B centromere by assaying a series of lines with different centromere breakpoints, and the markers were joined to make a ~10kb pseudocontig or B minimal map. Chromatin immunoprecipitation for CENH3 associated DNA was carried out in B73 lines with and without B chromosome. Centromere specific reads were mapped to the B minimal map and B73 genome to identify CRM2-TD marker sequences associated with the active centromere and 31 markers were found that span the centromere cores, necessary for centromere formation. Lack of these markers were associated with ectopic neocentromere formation. The genetic map and minimal map of the B centromere will be essential for further analyzing of centromere deletions lines and formation of a physical map spanning the entirety of the B centromere. TEs play numerous important roles for genome evolution and centromere sequence is an example for class I elements. Non-autonomous derivatives of class II DNA transposons are called Miniature Inverted-Repeat Transposable Elements (MITE) and contribute to genetic diversity in maize. In the grasses, MITEs are abundant in the 3’ and 5’ regions of genes and associated with high gene expression. In this study, superfamilies of MITEs were analyzed by whether or not they act as boundary elements between genes and a group of class I TEs shown to spread heterochromatin into nearby low-copy regions. We found that when a MITE is present between a gene and spreading TE, gene expression levels are higher and DNA methylation levels lower than when a MITE is absent. Methylation levels drastically reduce over a subset of MITE superfamilies, and these MITEs have a unique chromatin profile and sequence content.

Subjects/Keywords: Zea mays; centromere; MITE; transposable elements

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APA (6^th Edition):

Ellis, N. A. (2016). Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/34181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ellis, Nathanael Andrew. “Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize.” 2016. Thesis, University of Georgia. Accessed January 16, 2021. http://hdl.handle.net/10724/34181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ellis, Nathanael Andrew. “Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize.” 2016. Web. 16 Jan 2021.

Vancouver:

Ellis NA. Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize. [Internet] [Thesis]. University of Georgia; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10724/34181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ellis NA. Examining the chromatin profile at transposon-gene boundaries and developing a genetic map of the B centromere in maize. [Thesis]. University of Georgia; 2016. Available from: http://hdl.handle.net/10724/34181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

King Abdullah University of Science and Technology

17. Atinbayeva, Nazerke. Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation.

Degree: 2018, King Abdullah University of Science and Technology

URL: http://hdl.handle.net/10754/627885

► There are two classes of transposable elements: DNA transposons and retrotransposons. DNA transposons spread in the genome by “cut and paste” mechanism. In contrast, retrotransposons… (more)

▼ There are two classes of transposable elements: DNA transposons and retrotransposons. DNA transposons spread in the genome by “cut and paste” mechanism. In contrast, retrotransposons use copy and paste strategy involving RNA and retrotranscriptase mediated mechanism; these include long interspersed nuclear elements-1 (LINE-1, L1) and short interspersed nuclear elements (SINE). In mammals, in order to maintain genome integrity both types of transposons are tightly repressed. However, some copies of retrotransposons are still active in germ cells contributing to natural variation. Surprisingly, recent reports indicate that also somatic cells support L1 reactivation in early development, in particular in the brain leading to mosaicism. However, whether L1 retrotransposition is a part of other cell lineage developmental programs and its functional significance in the context of cell differentiation remain to be elucidated. To address this question, I investigated whether L1 retrotransposition was occurring during in vitro osteogenic and adipogenic differentiation of bone marrow derived human mesenchymal stem cells (hMSCs). Interestingly, clinical observations have revealed loss of bone density in HIV-infected individuals treated with nucleoside analogs that inhibit HIV retrotranscriptase, as well as the endogenous one encoded by L1s. This observation made us to hypothesize that transposable elements played a positive role in post-natal bone homeostasis. I found that while adipogenesis is “retrotransposition free”, osteogenic differentiation is a “retrotransposition-prone” process and its inhibition blocks its genetic program. Indeed, L1 DNA content does not change during adipogenic differentiation and that of retrotranscriptase does not have any effect on the acquisition of a terminally differentiated phenotype. In contrast, soon after MSCs commitment into pre-osteoblasts, L1 retrotransposable elements increase their expression and actively transpose. Inhibition of retrotransposition and knock down of L1 mRNA strongly impairs matrix deposition. Moreover, I forced L1 expression in in vitro adipogenesis, by directly delivering L1 mRNA to the cells. Interestingly, overexpression of L1 elements was detrimental for in vitro adipogenesis. Then, I performed loss of function experiments in osteogenesis by directly targeting and degrading the L1 endogenous transcript. This experiment confirmed the positive role of L1 reactivation in the osteogenic context, suggesting also a possible role for L1 RNA, distinct from retrotransposition.

Subjects/Keywords: transposable elements; osteogenic; adipogenic; LINE-1; retrotransposition

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Atinbayeva, N. (2018). Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation. (Thesis). King Abdullah University of Science and Technology. Retrieved from http://hdl.handle.net/10754/627885

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Atinbayeva, Nazerke. “Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation.” 2018. Thesis, King Abdullah University of Science and Technology. Accessed January 16, 2021. http://hdl.handle.net/10754/627885.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Atinbayeva, Nazerke. “Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation.” 2018. Web. 16 Jan 2021.

Vancouver:

Atinbayeva N. Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation. [Internet] [Thesis]. King Abdullah University of Science and Technology; 2018. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10754/627885.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Atinbayeva N. Ectopic expression and knocking-down of LINE-1 mRNA in human mesenchymal stem cells: impact on in vitro osteogenic and adipogenic differentiation. [Thesis]. King Abdullah University of Science and Technology; 2018. Available from: http://hdl.handle.net/10754/627885

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

18. Simbeya, Christy Keziya. Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum.

Degree: 2015, University of Toronto

URL: http://hdl.handle.net/1807/69705

►

Miniature inverted-repeat transposable elements (MITEs) have been found to reach high copy numbers in eukaryotic genomes. The underlying mechanisms of their transposition and the characterization… (more)

Subjects/Keywords: bioinformatics; inverse PCR; Miniature inverted-repeat transposable elements; MITE amplification; Transposable elements; yeast; 0369

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Simbeya, C. K. (2015). Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/69705

Chicago Manual of Style (16^th Edition):

Simbeya, Christy Keziya. “Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum.” 2015. Masters Thesis, University of Toronto. Accessed January 16, 2021. http://hdl.handle.net/1807/69705.

MLA Handbook (7^th Edition):

Simbeya, Christy Keziya. “Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum.” 2015. Web. 16 Jan 2021.

Vancouver:

Simbeya CK. Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum. [Internet] [Masters thesis]. University of Toronto; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1807/69705.

Council of Science Editors:

Simbeya CK. Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum. [Masters Thesis]. University of Toronto; 2015. Available from: http://hdl.handle.net/1807/69705

19. Elliott, Tyler Adam. Conceptual and empirical investigations of eukaryotic transposable element evolution.

Degree: PhD, Department of Integrative Biology, 2017, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10154

► Transposable elements (TEs), mobile pieces of self-replicating DNA, are one of the driving forces behind genomic evolution in eukaryotic organisms. Their contribution to genome size… (more)

Subjects/Keywords: Evolution; Transposable Elements; Genomes; Selfish DNA; Evolution; Transposable Elements; Genomes; Selfish DNA

10 more images…

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APA (6^th Edition):

Elliott, T. A. (2017). Conceptual and empirical investigations of eukaryotic transposable element evolution. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10154

Chicago Manual of Style (16^th Edition):

Elliott, Tyler Adam. “Conceptual and empirical investigations of eukaryotic transposable element evolution.” 2017. Doctoral Dissertation, University of Guelph. Accessed January 16, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10154.

MLA Handbook (7^th Edition):

Elliott, Tyler Adam. “Conceptual and empirical investigations of eukaryotic transposable element evolution.” 2017. Web. 16 Jan 2021.

Vancouver:

Elliott TA. Conceptual and empirical investigations of eukaryotic transposable element evolution. [Internet] [Doctoral dissertation]. University of Guelph; 2017. [cited 2021 Jan 16]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10154.

Council of Science Editors:

Elliott TA. Conceptual and empirical investigations of eukaryotic transposable element evolution. [Doctoral Dissertation]. University of Guelph; 2017. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10154

University of Manchester

20. Manee, Manee. Comparative Genomics of Noncoding DNA.

Degree: 2016, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:298877

► High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust… (more)

▼ High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust indicators of functionally constrained elements. Nevertheless, the function of only a small fraction of such CNEs is known and their role in genome biology remains largely a mystery. Comparative genomics analysis in model organisms can shed light on CNE function and evolution of noncoding DNA in general. Recently, it has been reported that short CNEs in the Drosophila genome are typically very AT-rich but have unusually high levels of GC content in a much larger (~500 bp) window around them. To understand whether these “side effects” are dependent on their CNE definition or are a more general feature of the Drosophila genome, we analysed base composition of CNEs from two different CNE detection methods. We found side effects are real, but are restricted to a subset of CNEs in the genome. An alternative hypothesis to explain the existence of CNEs is the mutational cold spot hypothesis. Previous work using SNPs was shown evidence that CNEs are not mutational cold spots. Here, non-reference transposable elements (TEs) were used to test cold spot hypothesis. A significant reduction in levels of non-reference TEs was found in intronic and intergenic CNEs compared to the expected number of insertions. TEs in intergenic CNEs were also found at lower allele frequencies than TEs in intergenic spacers. Furthermore, we used simulation to explore the effects of insertion/deletion (indel) evolution on noncoding DNA sequences with and without constrained noncoding elements. We assessed several indel-capable simulators to test expected outcomes with no selectively constrained elements. Simulations with constrained elements show that sequences grow in length even when the deletion rate is exactly the same as the insertion rate. This result can be interpreted as being due to purifying selection on CNEs acting to remove an excess of deletion over insertions. Together, the results presented here provide insights into the evolution of noncoding DNA in one of the most important model organisms. Advisors/Committee Members: HUBBARD, SIMON SJ, Hubbard, Simon, Bergman, Casey.

Subjects/Keywords: Drosophila Genome; Noncoding DNA; Conserved Noncoding Elements; Transposable Elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Manee, M. (2016). Comparative Genomics of Noncoding DNA. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:298877

Chicago Manual of Style (16^th Edition):

Manee, Manee. “Comparative Genomics of Noncoding DNA.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 16, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:298877.

MLA Handbook (7^th Edition):

Manee, Manee. “Comparative Genomics of Noncoding DNA.” 2016. Web. 16 Jan 2021.

Vancouver:

Manee M. Comparative Genomics of Noncoding DNA. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 16]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:298877.

Council of Science Editors:

Manee M. Comparative Genomics of Noncoding DNA. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:298877

University of Manchester

21. Manee, Manee. Comparative genomics of noncoding DNA.

Degree: PhD, 2016, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764487

► High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust… (more)

▼ High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust indicators of functionally constrained elements. Nevertheless, the function of only a small fraction of such CNEs is known and their role in genome biology remains largely a mystery. Comparative genomics analysis in model organisms can shed light on CNE function and evolution of noncoding DNA in general. Recently, it has been reported that short CNEs in the Drosophila genome are typically very AT-rich but have unusually high levels of GC content in a much larger (~500 bp) window around them. To understand whether these "side effects" are dependent on their CNE definition or are a more general feature of the Drosophila genome, we analysed base composition of CNEs from two different CNE detection methods. We found side effects are real, but are restricted to a subset of CNEs in the genome. An alternative hypothesis to explain the existence of CNEs is the mutational cold spot hypothesis. Previous work using SNPs was shown evidence that CNEs are not mutational cold spots. Here, non-reference transposable elements (TEs) were used to test cold spot hypothesis. A significant reduction in levels of non-reference TEs was found in intronic and intergenic CNEs compared to the expected number of insertions. TEs in intergenic CNEs were also found at lower allele frequencies than TEs in intergenic spacers. Furthermore, we used simulation to explore the effects of insertion/deletion (indel) evolution on noncoding DNA sequences with and without constrained noncoding elements. We assessed several indel-capable simulators to test expected outcomes with no selectively constrained elements. Simulations with constrained elements show that sequences grow in length even when the deletion rate is exactly the same as the insertion rate. This result can be interpreted as being due to purifying selection on CNEs acting to remove an excess of deletion over insertions. Together, the results presented here provide insights into the evolution of noncoding DNA in one of the most important model organisms.

Subjects/Keywords: Drosophila Genome; Noncoding DNA; Conserved Noncoding Elements; Transposable Elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Manee, M. (2016). Comparative genomics of noncoding DNA. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764487

Chicago Manual of Style (16^th Edition):

Manee, Manee. “Comparative genomics of noncoding DNA.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 16, 2021. https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764487.

MLA Handbook (7^th Edition):

Manee, Manee. “Comparative genomics of noncoding DNA.” 2016. Web. 16 Jan 2021.

Vancouver:

Manee M. Comparative genomics of noncoding DNA. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 16]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764487.

Council of Science Editors:

Manee M. Comparative genomics of noncoding DNA. [Doctoral Dissertation]. University of Manchester; 2016. Available from: https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764487

University of Toronto

22. Wong, Amy. Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti.

Degree: 2011, University of Toronto

URL: http://hdl.handle.net/1807/31635

►

Miniature Inverted-repeat Transposable Elements (MITEs) are a type of transposable element (TE) that lacks coding capacity. It has been established that in rice that certain… (more)

Subjects/Keywords: Transposable element; Miniature inverted repeat transposable elements; Tc1/Mariner; Aedes aegypti; Stowaway; 0307; 0715

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wong, A. (2011). Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/31635

Chicago Manual of Style (16^th Edition):

Wong, Amy. “Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti.” 2011. Masters Thesis, University of Toronto. Accessed January 16, 2021. http://hdl.handle.net/1807/31635.

MLA Handbook (7^th Edition):

Wong, Amy. “Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti.” 2011. Web. 16 Jan 2021.

Vancouver:

Wong A. Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti. [Internet] [Masters thesis]. University of Toronto; 2011. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1807/31635.

Council of Science Editors:

Wong A. Establishing the Functional Links between Stowaway-like MITEs and Transposases Belonging to the Tc1/Mariner Superfamily in the Yellow Fever Mosquito, Aedes aegypti. [Masters Thesis]. University of Toronto; 2011. Available from: http://hdl.handle.net/1807/31635

23. Saint leandre, Bastien. La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic.

Degree: Docteur es, Sciences de la vie et de la santé, 2016, Université Paris-Saclay (ComUE)

URL: http://www.theses.fr/2016SACLS084

►

Les Eléments Transposables (ET) sont des parasites du génome caractérisés par leur capacité à se répliquer plus rapidement que les autres éléments génétiques du génome.… (more)

▼

Les Eléments Transposables (ET) sont des parasites du génome caractérisés par leur capacité à se répliquer plus rapidement que les autres éléments génétiques du génome. La régulation par la voie des piARN joue un rôle essentiel pour limiter l’expansion des ET dans les lignées germinales des animaux.La première question posée est comment le génome répond face à une nouvelle invasion par un ET. Dans ce but, nous avons introduit le transposon de Classe II mariner (sous-famille mos1) chez D. melanogaster, qui ne contient naturellement pas l’élément. Nous avons montré, qu’après son amplification autonome dans le génome, l’élément avait atteint un équilibre en termes de nombre de copies, depuis qu’une régulation de novo par les piARN avait été acquise.Deuxièmement, nous avons étudié la mobilisation de l’élément mariner au cours du processus de colonisation des régions géographiques tempérées. A partir d’un large panel de populations naturelles nous avons trouvé que l’activité moyenne de mariner était remarquablement augmentée dans les populations non-Africaines en comparaison aux populations Africaines. Ces variations peuvent s’expliquer par un fort polymorphisme d’expression (transcriptionnel et traductionnel) des gènes de la voie des piARN.Le troisième chapitre soutient que la forte activité des ET dans la lignée germinale mâle est un phénomène global chez les drosophiles. Par ailleurs, le contenu en ET chez les espèces sœurs (D. melanogaster et D. simulans) a fortement divergé et, cela a affecté la réponse associée à la production des piARN. Chez D. melanogaster, de nombreux « burst » de transposition ont eut lieu récemment. Ces familles d’ET sont activement réprimées par les piARN dans l’ovaire et donc, se retrouvent massivement surexprimés dans les testicules. Chez D. simulans, nous pensons que la réponse par les piARN résulte principalement d’une régulation passée qui semble être la relique d’anciennes invasions d’ET.La voie des piARN est supposé être « garante de l’intégrité du génome » de par son rôle actif dans la défense contre les ET. Cependant, si la sélection naturelle purge les génomes de ces parasites délétères, il semble que les mécanismes de régulation de l’hôte contribuent au maintien de l’homéostasie du génome en limitant leur expansion, et quelque part en favoriser le maintien sur long terme. Ainsi, une autre interprétation pourrait être que la voie des piARN est « garante de la diversification du génome » de par son rôle à faciliter l’accumulation des ET.

Transposable Elements (TEs) are genomic parasites characterized by their ability to replicate faster than any other genetic element in the genomes. The piRNA mediated silencing is of central importance to limit TE expansion in the germline of animal species. The present dissertation explores the relationship between TEs and piRNAs alongside their evolutionary dynamics.The first question raised here was to understand how the genome responds to a new TE invasion. For that purpose, we injected a mariner Class II transposon into D. melanogaster genome…

Advisors/Committee Members: Capy, Pierre (thesis director), Hua-Van, Aurélie (thesis director).

Subjects/Keywords: PiARN; Elements Transposable; Lignée germinale; Epigénétique; Régulation; Mariner; PiRNA; Transposable Element; Germline; Epigenetic; Regulation; Mariner

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saint leandre, B. (2016). La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic. (Doctoral Dissertation). Université Paris-Saclay (ComUE). Retrieved from http://www.theses.fr/2016SACLS084

Chicago Manual of Style (16^th Edition):

Saint leandre, Bastien. “La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic.” 2016. Doctoral Dissertation, Université Paris-Saclay (ComUE). Accessed January 16, 2021. http://www.theses.fr/2016SACLS084.

MLA Handbook (7^th Edition):

Saint leandre, Bastien. “La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic.” 2016. Web. 16 Jan 2021.

Vancouver:

Saint leandre B. La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic. [Internet] [Doctoral dissertation]. Université Paris-Saclay (ComUE); 2016. [cited 2021 Jan 16]. Available from: http://www.theses.fr/2016SACLS084.

Council of Science Editors:

Saint leandre B. La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition : Transposable element under piRNA genes regulation in Drosophila : male and female germline differences and their consequences for transposition dynamic. [Doctoral Dissertation]. Université Paris-Saclay (ComUE); 2016. Available from: http://www.theses.fr/2016SACLS084

Université Paris-Sud – Paris XI

24. Etcheverry, Mathilde. Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana.

Degree: Docteur es, Biologie, 2013, Université Paris-Sud – Paris XI

URL: http://www.theses.fr/2013PA112208

► Les éléments transposables (ET) et leur reliques sont des composants majeurs des génomes eucaryotes. Ils sont potentiellement hautement mutagéniques car leur prolifération peut engendrer des… (more)

▼ Les éléments transposables (ET) et leur reliques sont des composants majeurs des génomes eucaryotes. Ils sont potentiellement hautement mutagéniques car leur prolifération peut engendrer des réarrangements chromosomiques, des interruptions de gènes ou affecter l’expression génique par interférence transcriptionnelle. Néanmoins, peu d’ET sont généralement mobiles dans les génomes grâce à l’action de mécanismes qui restreignent leur activité comme la méthylation de l’ADN chez les mammifères et les plantes. De fait, chez Arabidopsis thaliana, une perte sévère de méthylation de l’ADN causée par une mutation dans le gène codant la protéine remodeleuse de chromatine DDM1 (DECREASE IN DNA METHYLATION 1) engendre l’accumulation massive de transcrits correspondants à des séquences d’ET. En revanche, peu d’ET semblent être mobilisés suite à cette réactivation transcriptionnelle. Nous proposons ici de déterminer (1) l’étendue de la mobilisation des ET suite à la perte de méthylation de l’ADN, (2) la distribution des nouvelles insertions d’ET le long du génome d’Arabidopsis et (3) les conséquences des nouvelles insertions d’ET sur l’expression des gènes situés à proximité. Dans ce but, nous avons séquencé le génome d’une cinquantaine d’epiRIL (epigenetic Recombinant Inbred Lines) dérivées d’un croisement entre une plante sauvage et un mutant ddm1. Suite au croisement retour de la F1 avec une plante sauvage et sélection des individus F2 homozygotes pour l’allèle sauvage DDM1, les epiRIL ont été propagées au travers de 6 autofécondations successives. Les epiRIL permettent donc l’étude détaillée des évènements de transpositions juste après qu’ils aient eu lieu. Pour identifier les évènements de transpositions dans ces lignées nous avons mis au point TE-tracker, un programme basé sur les données issues du séquençage Illumina de banques maite-pair. Par cette approche, nous avons montré que les ET mobiles dans ddm1 et les epiRIL appartiennent à seulement une quinzaine environ des >300 familles identifiées dans le génome d’Arabidopsis. Qui plus est, on observe des variations importantes de fréquences et dynamiques de transpositions entre les différentes familles d’ET ce qui suggère l’existence de mécanismes additionnels contrôlant la transposition. Les analyses moléculaires réalisées sur un sous-ensemble des ET mobilisés appartenant à différentes familles ont notamment montré que ces différences sont dues en grande partie aux différentes modalités d’établissement du contrôle épigénétique sur les ET nouvellement insérés. D’autre part, nos analyses indiquent que la distribution des nouvelles insertions d’ET diffère grandement de celle des copies résidentes. Ce résultat suggère donc que la suraccumulation des séquences d’ET dans les régions péricentromériques du génome d’Arabidopsis n’est pas due à un ciblage spécifique des insertions dans ces régions, mais est plutôt la conséquence de leur élimination des bras chromosomiques. Enfin, nous avons cherché à déterminer dans quelle mesure la méthylation de l’ADN associée aux séquences répétées… Advisors/Committee Members: Colot, Vincent (thesis director).

Subjects/Keywords: Elément transposable; Méthylation de l’ADN; Épigénétique; EpiRIL; Transposable elements; DNA methylation; Epigenetics; EpiRIL

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Etcheverry, M. (2013). Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana. (Doctoral Dissertation). Université Paris-Sud – Paris XI. Retrieved from http://www.theses.fr/2013PA112208

Chicago Manual of Style (16^th Edition):

Etcheverry, Mathilde. “Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana.” 2013. Doctoral Dissertation, Université Paris-Sud – Paris XI. Accessed January 16, 2021. http://www.theses.fr/2013PA112208.

MLA Handbook (7^th Edition):

Etcheverry, Mathilde. “Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana.” 2013. Web. 16 Jan 2021.

Vancouver:

Etcheverry M. Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana. [Internet] [Doctoral dissertation]. Université Paris-Sud – Paris XI; 2013. [cited 2021 Jan 16]. Available from: http://www.theses.fr/2013PA112208.

Council of Science Editors:

Etcheverry M. Etude du contrôle des éléments transposables par la méthylation de l’ADN chez Arabidopsis thaliana : Assessing the control of transposable elements by DNA methylation in Arabidopsis thaliana. [Doctoral Dissertation]. Université Paris-Sud – Paris XI; 2013. Available from: http://www.theses.fr/2013PA112208

25. Saccaro Junior, Nilo Luiz. O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz.

Degree: Mestrado, Botânica, 2007, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/ ;

►

Os elementos transponíveis (TEs) constituem grande parte do material genético de diversos eucariotos, alcançando entre 50-80% do genoma de gramíneas. Os projetos genoma proporcionaram um… (more)

▼

Os elementos transponíveis (TEs) constituem grande parte do material genético de diversos eucariotos, alcançando entre 50-80% do genoma de gramíneas. Os projetos genoma proporcionaram um aumento das informações disponíveis sobre estes elementos, o que evidenciou sua importância e possibilitou o desenvolvimento de novas abordagens para seu estudo. O sistema Mutator (Mu) de milho é o mais ativo e mutagênico transposon de plantas. Além do elemento autônomo, MuDR, o sistema compreende ainda um conjunto de elementos bastante heterogêneo em sua seqüência e estrutura, chamados MuLEs, que podem conter até mesmo fragmentos de genes do hospedeiro. As seqüências de transposons mais abundantemente expressas no transcriptoma de cana-de-açúcar são relacionadas a MuDR e se agrupam em quatro clados (nomeados Classes I, II, II e IV), existentes antes da divergência entre Mono e Eudicotiledôneas. O trabalho apresentado aqui teve o objetivo de aprofundar o conhecimento sobre o sistema Mutator em cana-de-açúcar a partir da análise comparativa entre seqüências dessa planta e de arroz (cujo genoma está totalmente seqüenciado). Foi possível avaliar a abundância e diversidade do sistema Mu em gramíneas, ficando evidente uma amplificação de elementos clado-específica, tendo a Classe II sofrido uma explosão no número de cópias ao longo da evolução destas plantas. Análises estruturais revelaram que, enquanto as Classes I e II compreendem elementos com características de transposons, as Classes III e IV são, na verdade, transposases domesticadas. Foram completamente seqüenciados dois clones de BAC de cana-de-açúcar, um proveniente de cada parental do híbrido (Saccharum officinarum e Saccharum spontaneum), ambos contendo elementos da Classe III. Estes elementos foram caracterizados e a seqüência genômica de cana foi comparada com sua ortóloga em arroz, revelando um acúmulo de TEs nas regiões intergênicas.

Transposable elements (TEs) constitute great part of eukaryote genetic material, in grasses, they comprise between 50-80% of the genome. Genome projects have significantly increased the amount of information about these elements, revealing their importance and allowing the development of new approaches for their study. The Mutator system (Mu) of maize is the most active and mutagenic plant transposon. Beyond the autonomous element, MuDR, the system comprises a very heterogeneous, in sequence and structure, set of elements, called MuLEs, that can contain even host gene fragments. The most abundant transposon related sequences expressed in sugarcane transcriptoma are the MuDR-like. They group into four clades (called Classes I, II, III and IV) that exist prior to the Mono and Eudicot split. The aim of this work is to gain knowledge about the Mutator system in sugarcane through the comparative analysis against rice (whose genome is completely sequenced). The results described the abundance and diversity of the Mu system in grasses, evidencing a clado-specific amplification with a burst of Class II along the evolution of this plant group.…

Advisors/Committee Members: Rossi, Maria Magdalena.

Subjects/Keywords: Saccharum; Saccharum; Elementos de transposição; Genômica; Genomics; Transposable elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saccaro Junior, N. L. (2007). O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/ ;

Chicago Manual of Style (16^th Edition):

Saccaro Junior, Nilo Luiz. “O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz.” 2007. Masters Thesis, University of São Paulo. Accessed January 16, 2021. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/ ;.

MLA Handbook (7^th Edition):

Saccaro Junior, Nilo Luiz. “O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz.” 2007. Web. 16 Jan 2021.

Vancouver:

Saccaro Junior NL. O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz. [Internet] [Masters thesis]. University of São Paulo; 2007. [cited 2021 Jan 16]. Available from: http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/ ;.

Council of Science Editors:

Saccaro Junior NL. O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz. [Masters Thesis]. University of São Paulo; 2007. Available from: http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/ ;

University of California – Merced

26. Banuelos, Mario. Developing Statistical Models for the Analysis of Genomic Variants.

Degree: Applied Mathematics, 2018, University of California – Merced

URL: http://www.escholarship.org/uc/item/5278p7dz

► I develop a number of mathematical and statistical models for the study of genomic variation within and between species. These variants affect an organism's susceptibility… (more)

Subjects/Keywords: Applied mathematics; Biostatistics; mathematical modeling; optimization; structural variation detection; transposable elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Banuelos, M. (2018). Developing Statistical Models for the Analysis of Genomic Variants. (Thesis). University of California – Merced. Retrieved from http://www.escholarship.org/uc/item/5278p7dz

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Banuelos, Mario. “Developing Statistical Models for the Analysis of Genomic Variants.” 2018. Thesis, University of California – Merced. Accessed January 16, 2021. http://www.escholarship.org/uc/item/5278p7dz.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Banuelos, Mario. “Developing Statistical Models for the Analysis of Genomic Variants.” 2018. Web. 16 Jan 2021.

Vancouver:

Banuelos M. Developing Statistical Models for the Analysis of Genomic Variants. [Internet] [Thesis]. University of California – Merced; 2018. [cited 2021 Jan 16]. Available from: http://www.escholarship.org/uc/item/5278p7dz.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Banuelos M. Developing Statistical Models for the Analysis of Genomic Variants. [Thesis]. University of California – Merced; 2018. Available from: http://www.escholarship.org/uc/item/5278p7dz

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manchester

27. Nelson, Michael. Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila.

Degree: 2016, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:295594

► Transposable elements (TEs) are mutagenic mobile DNA sequences whose excision and insertion are powerful drivers of evolution. Some TE families are known to target specific… (more)

▼ Transposable elements (TEs) are mutagenic mobile DNA sequences whose excision and insertion are powerful drivers of evolution. Some TE families are known to target specific genome features, and studying their insertion preferences can provide information about both TE biology and the state of the genome at these locations. To investigate this, collecting large numbers of insertion sites for TEs in natural populations is required. Genome resequencing data can potentially provide a rich source of such insertion sites. The field of detecting these “non-reference” TE insertions is an active area of research, with many methods being released and no comprehensive review performed. To drive forward knowledge of TE biology and the field of non-reference TE detection, we created McClintock, an integrated pipeline of six TE detection methods. McClintock lowers the barriers against use of these methods by automating the creation of the diverse range of input files required whilst also setting up all methods to run simultaneously and standardising the output. To test McClintock and its component methods, it was run on both simulated and real Saccharomyces cerevisiae data. Tests on simulated data reveal the general properties of component methods’ predictions as well as the limitations of simulated data for testing software systems. Overlap between results from the McClintock component methods show many insertions detected by only one method, highlighting the need to run multiple TE detection methods to fully understand a resequenced sample. Utilising the well characterised properties of S. cerevisiae TE insertion preferences, real yeast population resequencing data can act as a biological validation for the predictions of McClintock. All component methods recreated previously known biological properties of S. cerevisiae TE insertions in natural population data. To demonstrate the versatility of McClintock, we applied the system to Drosophila melanogaster resequencing data. 27 Schneider’s cell lines were sequenced and analysed with McClintock. In addition to demonstrating the scalability of McClintock to larger genomes with more TE families, this exposed ongoing transposition in S2 cell lines. Likewise, the use of non-reference TE insertions as variable sites allowed us to recreate the relationships between S2 sub-lines, confirming that S1, S2, and S3 were most likely established separately. The results also suggest that there are several S2 sub-lines in use and that these sub-lines can differ from each other in TE content by hundreds of non-reference TE copies. Overall this thesis demonstrates that the McClintock pipeline can highlight problems in TE detection from genome data as well as revealing that much can still be learned from this data source. Advisors/Committee Members: RONSHAUGEN, MATTHEW M, Ronshaugen, Matthew, Bergman, Casey.

Subjects/Keywords: Bioinformatics; Transposable Elements; Drosophila melanogaster; Saccharomyces cerevisiae; McClintock

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nelson, M. (2016). Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:295594

Chicago Manual of Style (16^th Edition):

Nelson, Michael. “Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 16, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:295594.

MLA Handbook (7^th Edition):

Nelson, Michael. “Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila.” 2016. Web. 16 Jan 2021.

Vancouver:

Nelson M. Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 16]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:295594.

Council of Science Editors:

Nelson M. Bioinformatic Approaches to Detect Transposable Element Insertions in High Throughput Sequence Data from Saccharomyces and Drosophila. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:295594

Cornell University

28. Rajavasireddy, Satyaki. The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna.

Degree: PhD, Molecular and Cell Biology, 2014, Cornell University

URL: http://hdl.handle.net/1813/36181

► Heterochromatin keeps in check selfish elements such as transposable elements (TEs) and satellite DNAs, which can wreak havoc on a genome by mobilizing and increasing… (more)

▼ Heterochromatin keeps in check selfish elements such as transposable elements (TEs) and satellite DNAs, which can wreak havoc on a genome by mobilizing and increasing their copy number, leading to genomic instability and sterility. Heterochromatin proteins (HPs) that mediate repression of selfish DNA may therefore be in an eternal arms race with selfish DNA. This arms race might explain the extensive sequence divergence discovered in some HPs which cause post-zygotic reproductive isolation. However, evidence for this model is limited. For my thesis work, I studied Lhr, a strong candidate gene, to test this model. Lhr encodes a rapidly evolving, HP1a interacting, HP that causes lethality in hybrids between D. melanogaster and D. simulans. To determine Lhr's normal function we knocked-out Lhr via homologous recombination in D. melanogaster. I discovered that Lhr mutant females have reduced fertility. Using mRNA-Seq, I found that Lhr regulates the steady state levels of many different satellite and TE transcripts. ChIP data argue that this increase is due to a defective post-transcriptional pathway. However, my analysis of small RNA-Seq data shows that small RNAs targeting most misregulated transposable elements are not affected and suggests instead that Lhr functions independently or downstream of the small RNA pathway. To address the effects of extensive sequence divergence of Lhr between D. melanogaster and D. simulans, I performed a RNA-Seq comparison of wildtype and Lhr mutant D. simulans lines. I discovered that loss of Lhr upregulates different transposable elements in D. melanogaster and D. simulans. Further, comparing the two species, I made the striking observation that localization of Lhr protein has expanded in D. melanogaster to encompass two satellites which account for nearly 6% of the D. melanogaster genome, but only 0.7% in the inferred ancestor of D. melanogaster and D. simulans. Finally, I found that Lhr is required for expression of heterochromatic genes, suggesting that it helps the host genes in D. melanogaster to adapt to the greatly expanded heterochromatic content of this species. My studies uncover an important component of the machinery that an organism uses to repress TEs and satellites, and to adapt to changes in selfish DNA. My work further demonstrates that each Lhr ortholog has adapted to repress different selfish elements in each species and provides support for the arms race model. Advisors/Committee Members: Barbash, Daniel A. (chair), Lis, John T (committee member), Soloway, Paul (committee member).

Subjects/Keywords: Heterochromatin Lhr Drosophila; Hybrid Incompatibility; Satellites Transposable elements

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rajavasireddy, S. (2014). The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/36181

Chicago Manual of Style (16^th Edition):

Rajavasireddy, Satyaki. “The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna.” 2014. Doctoral Dissertation, Cornell University. Accessed January 16, 2021. http://hdl.handle.net/1813/36181.

MLA Handbook (7^th Edition):

Rajavasireddy, Satyaki. “The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna.” 2014. Web. 16 Jan 2021.

Vancouver:

Rajavasireddy S. The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1813/36181.

Council of Science Editors:

Rajavasireddy S. The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/36181

29. McGurk, Michael Peter. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.

Degree: PhD, Biochemistry, Molecular and Cell Biology, 2019, Cornell University

URL: http://hdl.handle.net/1813/67819

► Eukaryotic genomes are replete with repeated sequence, in the form of transposable elements (TEs) dispersed throughout genomes and as large stretches of tandem repeats (satellite… (more)

▼ Eukaryotic genomes are replete with repeated sequence, in the form of transposable elements (TEs) dispersed throughout genomes and as large stretches of tandem repeats (satellite arrays). Neutral and selfish evolution likely explain their prevalence, but repeat variation can impact function by altering gene expression, influencing chromosome segregation, and even creating reproductive barriers between species. Yet, while population genomic analyses have illuminated the function and evolution of much of the genome, our understanding of repeat evolution lags behind. Tools that uncover population variation in non-repetitive portions of genomes often fail when applied to repetitive sequence. To extend structural variant discovery to the repetitive component of genomes we developed ConTExt, employing mixture modelling to discover structural variation in repetitive sequence from the short read data that commonly comprises available population genomic data. We first applied ConTExt to investigate how mobile genetic parasites can transform into megabase-sized tandem arrays, as some satellites clearly originated as TEs. Making use of the Global Diversity Lines, a panel of Drosophila melanogaster strains from five populations, this study revealed an unappreciated consequence of transposition: an abundance of TE tandem dimers resulting from TEs inserting multiple times at the same locus. Thus, the defining characteristic of TEs—transposition—regularly generates structures from which new satellite arrays can arise, and we further captured multiple stages in the emergence of satellite arrays ongoing in a single species. We then investigated the complex array of processes which shape TE evolution, focusing on the putatively domesticated HeT-A, TAHRE, and TART (HTT) elements that maintain the telomeres of Drosophila. To provide context, we compared HTT variation to that of other TE families with known properties. Our results suggest that differences between HTT variation and other TE families largely result from the rapid sequence turnover at telomeres. We further suggest that the localization of the HTTs to the telomere reflects a successful evolutionary strategy rather than pure domestication. However, we find evidence that susceptibility to host regulation varies among HTTs and across populations, suggesting that despite constituting the mechanism of telomere maintenance, the HTTs remain in conflict with the genome like any other TE. Advisors/Committee Members: Barbash, Daniel A. (chair), Clark, Andrew (committee member), Soloway, Paul (committee member).

Subjects/Keywords: Repetitive DNA; Satellite DNA; Transposable elements; Evolution & development; Genetics; Bioinformatics

10 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McGurk, M. P. (2019). Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/67819

Chicago Manual of Style (16^th Edition):

McGurk, Michael Peter. “Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.” 2019. Doctoral Dissertation, Cornell University. Accessed January 16, 2021. http://hdl.handle.net/1813/67819.

MLA Handbook (7^th Edition):

McGurk, Michael Peter. “Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.” 2019. Web. 16 Jan 2021.

Vancouver:

McGurk MP. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1813/67819.

Council of Science Editors:

McGurk MP. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/67819

Texas A&M University

30. Yang, Guojun. Miniature inverted repeat transposable elements in rice - origin and function.

Degree: PhD, Biology, 2004, Texas A&M University

URL: http://hdl.handle.net/1969.1/318

► Transposable elements (TEs) are interspersed repetitive sequences that are present in most genomes. Miniature inverted repeat transposable elements (MITEs) are the most numerous Class II… (more)

Subjects/Keywords: MITE; transposable elements; MAK

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yang, G. (2004). Miniature inverted repeat transposable elements in rice - origin and function. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/318

Chicago Manual of Style (16^th Edition):

Yang, Guojun. “Miniature inverted repeat transposable elements in rice - origin and function.” 2004. Doctoral Dissertation, Texas A&M University. Accessed January 16, 2021. http://hdl.handle.net/1969.1/318.

MLA Handbook (7^th Edition):

Yang, Guojun. “Miniature inverted repeat transposable elements in rice - origin and function.” 2004. Web. 16 Jan 2021.

Vancouver:

Yang G. Miniature inverted repeat transposable elements in rice - origin and function. [Internet] [Doctoral dissertation]. Texas A&M University; 2004. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1969.1/318.

Council of Science Editors:

Yang G. Miniature inverted repeat transposable elements in rice - origin and function. [Doctoral Dissertation]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/318

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Open Access Theses and Dissertations