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Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Chromatin, the DNA/protein complex that makes up the major part of eukaryotic chromosomes, plays an important role in regulating many biological processes. Distinct patterns of histone occupancy correlate with different levels of transcriptional activity and with many functional elements. Modern high-throughput sequencing technology combined with chromatin immunoprecipitation (ChIP) has made it possible to profile histone modification patterns on a genome-wide scale for large mammalian genomes. In this thesis, I perform the first comprehensive comparison of histone modifications and nucleosome occupancy between D. melanogaster and H. sapiens. A systematic comparison among multiple organisms is challenging due to issues in integrating datasets derived from multiple platforms and technologies, but I show that proper normalization enables this comparison. My analysis reveals key differences in enrichment patterns of histone modifications, which are driven by differences in nucleosome occupancy. One biological system in which chromatin architecture plays a major role is Drosophila male dosage compensation, the process by which male X-linked genes are up-regulated to compensate for the lack of a second copy. Dosage compensation is regulated primarily by the Male-Specific Lethal (MSL) protein complex. However, the mechanisms by which MSL up-regulates X-linked genes and by which it specifically targets the X chromosome remain poorly understood. I performed analysis of Global Run-on Sequencing (GRO-seq) to determine the specific effect of MSL on the level of nascent transcripts in male Drosophila cells. My analysis indicates that MSL activity results in increased RNA polymerase density within the bodies of active X-linked genes, suggesting that regulation occurs at the level of transcriptional elongation. To further investigate the targeting mechanism of MSL, I examined expression and binding data for CLAMP (Coupling Lethal Adapter for MSL Proteins) a previously uncharacterized protein identified in a recent screen as a regulator of MSL. This analysis reveals that CLAMP exhibits a synergistic relationship with MSL and promotes X-chromosome specificity. Taken together, my results provide novel insights into the nature of the Drosophila chromatin landscape and the regulatory mechanism of dosage compensation. / 2031-01-01

O estudo da interação entre os indivíduos de uma mesma espécie ou de espécies diferentes é essencial para o entendimento das dinâmicas envolvidas na manutenção das comunidades ou assembléias na natureza. Assim, o estudo das preferências alimentares das larvas dos drosofilídeos, refletidas no padrão de emergência das mesmas dos sítios de oviposição, é de suma importância, uma vez que este grupo de organismos tornou-se um excelente modelo para o estudo de padrões ecológicos. Assim, esta tese busca identificar como as larvas de espécies de Drosophilidae se relacionam na utilização dos recursos tróficos, identificando quais os principais fatores que podem estar atuando na manutenção da diversidade de espécies de suas assembléias em áreas de Mata Atlântica e urbanas de Florianópolis (SC). Realizamos coletas de frutos em onze localidades do Estado de Santa Catarina, onde montamos uma listagem das espécies vegetais hospedeiras utilizadas como sítio de oviposição e das espécies de Drosophilidae que as utilizam. Observamos que as espécies de Drosophilidae colonizam os ambientes urbanos estudados, mas há uma perda de diversidade de espécies, evidenciada pela ausência de espécies raras nestas amostras. Ainda, as espécies de Drosophilidae coletadas apresentaram um caráter generalista quanto à utilização dos recursos tróficos, onde, nas assembléias de Mata Atlântica, verificou-se a formação de grupos ecológicos funcionais. Este tipo de organização não foi observado nas assembléias urbanas, onde há uma grande sobreposição dos nichos e uma menor diversidade de espécies. Além dos frutos, foram coletados também corpos de frutificação de fungos a fim de verificarmos as espécies de Drosophilidae emergentes dos mesmos. Dentre as espécies de moscas emergentes estão as dos gêneros Drosophila, Hirtodrosophila, Mycodrosophila e Leucophenga. Cabe ressaltar que as espécies neotropicais da radiação immigrans-tripunctata (gênero Drosophila) possuem a capacidade de colonizar fungos em ambientes preservados e alterados do bioma Mata Atlântica. Em outro estudo, buscamos verificar como a limitação de recursos alimentares para as larvas de drosofilídes pode influenciar a interação competitiva entre as mesmas. Para tal, foram coletados frutos de Buchenavia tomentosa (Combretaceae) e submetidos a dois tratamentos, um deles com uma suplementação alimentar. Assim, obtivemos evidências de que há restrições alimentares ou nutricionais em recursos naturais, que aumentam a interação competitiva entre espécies da família Drosophilidae. Entretanto, estas espécies possuem diferentes respostas à esta limitação, e o aumento da competição interespecífica parece ser maior que da intraespecífica. Finalmente, foi realizada uma revisão da ocorrência das espécies de Drosophilidae no Brasil, onde foram levantadas 304 espécies coletadas em nosso território. A maioria dos registros é de espécies do gênero Drosophila, o mais bem estudado da família. Os estados mais bem amostrados até o momento são São Paulo, Rio de Janeiro, Rio Grande do Sul e Santa Catarina, além do Distrito Federal, onde há grupos de pesquisa enfocando a ecologia e taxonomia das espécies de Drosophilidae. Esta revisão auxiliou na avaliação dos objetivos anteriores, contribuindo com um panorama do conhecimento e distribuição desta moscas no Brasil. / The study of the interaction among the individuals of a same species or of different ones is essential for the understanding of the dynamics involved in the communities or assemblies maintenance in nature. Thus, the study of the alimentary preferences of the drosophilids larvae, evidenciated by their emergency pattern of the breeding sites, is of highest importance once that this group of organisms became an excellent model for the study of ecological patterns. So, this thesis aimed to identify how the larvae of the Drosophilidae species use the trophic resources, identifying the main factors that can be acting in the maintenancement of the species diversity of assemblies in areas of Atlantic Rain Forest and urbanized of Florianópolis (SC). We collected fruits in eleven locations of the State of Santa Catarina, and we listed the vegetable host species used as breeding sites and the Drosophilidae species emerged of them. We observed that the Drosophilidae species colonize the studied urban environments, but there is a loss of species diversity, evidenced by the absence of rare species in these samples. Although, the collected Drosophilidae species presented a generalist character for the use of the trophic resources, where, the formation of functional ecological groups was verified in the assemblies of Atlantic Rain Forest. This kind of organization was not observed in the urban assemblies, where there are a high niche overlap and lower species diversity. Besides fruits collections, were carried out collections of fungi bodies of fructification in order to verify their emerging Drosophilidae species. Among the emerging fly species are the ones of the Drosophila, Hirtodrosophila, Mycodrosophila and Leucophenga genera. It to be useful to emphasize that the Neotropical species of the immigrans-tripunctata radiation (Drosophila genus) have capacity to colonize mushrooms in preserved Atlantic Rain Forest and antropic environments. In another study, we search for how the limitation in trophic resources for drosophilid larvae could influence the competitive interaction among them. For such, fruits of Buchenavia tomentosa (Combretaceae) were collected and submitted to two treatments, one of them with an alimentary supply. Thereby, we obtained evidences that there are alimentary or nutritional restrictions in natural resources, which increase the competitive interaction among species of the family Drosophilidae. However, these species have different answers to this limitation, and the increase of the interspecific competition seems to be larger than of the intraspecific. Finally, a revision of the occurrence of the Drosophilidae species in Brazil was accomplished, where were found 304 species recorded in our territory. Most of the records is of species of the Drosophila genus, the best studied of the family. The better evalueted states until the moment are São Paulo, Rio de Janeiro, Rio Grande do Sul and Santa Catarina, besides Distrito Federal, where there are research groups focusing the ecology and taxonomy of the Drosophilidae species. This revision helped us in the evaluation of the previous objectives, contributing with a panorama of the knowledge and distribution of these flies in Brazil.

"June 2003". / Bibliography: p. 189-196. / xv, 196 p. : ill. (some col.), plates (col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis aimed to characterise the G1-S phase role of Drosophila Eb1, dEb1, which was identified in a cyclin E genetic screen. A dominant modifier screen was undertaken to identify novel regulators of cyclin E, and cell cycle progression using a hypomorphic allele of cyclin E. One suppressor from this screen, Su(DmcycEjp)2.5, was identified as a potential Drosophila homologue of the microtubule binding protein Eb1, dEb1. Southern and northern analysis confirmed that Su(DmcycEjp)2.5 is an allele of dEb1, and other dEb1 alleles were shown to also be able to suppress cyclin Ejp. / Thesis (Ph.D.)--University of Adelaide, School of Molecular and Biomedical Sciences, 2003

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Thesis (Ph. D.)--University of Oregon, 2006. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 101-115). Also available for download via the World Wide Web; free to University of Oregon users.

The telomeres of most organisms are characterized by a protein-capping complex that protects chromosome ends, a series of repetitive subtelomeric sequences known as Telomere-Associated Sequences (TAS), and a behavioral phenomenon known as Telomere Position Effect (TPE). TPE is a phenomenon whereby normally active genes become repressed and silenced if relocated near to telomeres, and is thought to be a property of the proteins that constitute telomeric heterochromatin. Genetic dissection was used to exploit this phenomenon in order to identify components of telomeric heterochromatin in Drosophila melanogaster. Using genetic dissection, followed by a chromatin analysis technique known as Chromatin ImmunoPrecipitation (ChIP) I was able to identify three proteins, HDAC1, SU(VAR)3-9, and HP1c, as integral components of telomeric heterochromatin in Drosophila. HDAC1 and SU(VAR)3-9 are both believed to be involved in the gene-silencing process, and thus, their presence at telomeres could explain the phenomenon of TPE. Furthermore, I found that these proteins were specifically associated with the TAS region on the centromere-proximal side of the HeTA transposable elements that maintain telomere length in Drosophila. As a result of this, I proposed a model, which I call the ‘pairing-sliding model of telomere length control in Drosophila,’ which proposes that temporary incorrect pairing of Drosophila telomeres results in the deacetylation and subsequent methylation of the nucleosomes associated with the HeT-A and TART elements by TAS-associated HDAC1 and SU(VAR)3-9, resulting in these elements being transcriptionally silent. Thus, I propose that the TAS region, and the HDAC1 and SU(VAR)3-9 associated with it play a role in the negative regulation of telomere length in Drosophila.