Das Neuroblastom ist der dritthäufigste maligne Tumor im Kindesalter und ist für 15% der Todesfälle durch Krebs bei Kindern unter 14 Jahren verantwortlich. Viele molekularbiologische Vorgänge, die zu der heterogenen Prognose der Patienten beitragen, sind noch nicht verstanden. Als Hauptrisikomerkmal stellt sich die Amplifikation und erhöhte Expression von MYCN dar. In Vorarbeiten der Arbeitsgruppe von Prof. Christiansen zeigte MYCN Einfluss auf die Genregion von Thyroid Cancer 1 (TC1), das als neuer Marker für maligne Schilddrüsenkarzinome erkannt wurde. In der vorliegenden Arbeit wurden erste Untersuchungen zur prognostischen Bedeutung von TC1 im Neuroblastom, sowie die Charakterisierung eines TC1 Überexpressionsphänotyps humaner Neuroblastomzelllinien unter Einfluss von MYCN durchgeführt. Es wurde ein Überexpressionsvektor von TC1 in die Neuroblastomzelllinie SH-EP eingebracht, welche über ein aktivierbares MYCN- Konstrukt verfügt. Dieser neue Phänotyp wurde bezüglich der Proliferation, des Zellzyklus und der Apoptose im Vergleich zu einer Kontrollzelllinie ohne Überexpression untersucht. Eine In-silico Recherche in der Versteeg Neuroblastomdatenbank ergab eine deutlich bessere Überlebenswahrscheinlichkeit für Patientin mit hoher TC1 Expression. Es konnte gezeigt werden, dass MYCN Amplifikation und Expression in einem Panel von Neuroblastom Zelllinien nicht mit der TC1 Expression korrelieren. Die spezifische Aktivierung von MYCN führte hingegen zu einer Expressionssteigerung von TC1. Weiterhin zeigte sich, dass eine TC1 Überexpression die Proliferation hemmt, indem es die MYCN induzierte G1- S- Phasen- Transition inhibiert. TC1 zeigt antiproliferative Eigenschaften im Zellkulturmodell und stellt sich als neuer prognostisch günstiger Parameter im Neuroblastom dar.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Transposable elements (TEs) are DNA regions that can move within and between genomes, causing great impact on the host organisms. The Tc1-Mariner superfamily stands out for being, probably, the DNA transposons superfamily with greater distribution in nature, being ubiquitous in eukaryotes. In part of this work, we characterize elements of the mariner family in Neotropical drosophilids, which were obtained through amplification with degenerated primers. The primers were designed for the catalytic domain region of mariner transposase allowing amplification of a wide range of mariner-like sequences. A sum of twenty-three species have mariner-like sequences belonging to three subfamilies (mellifera, mauritiana and irritans). These elements present a patchy distribution and incongruences with the host phylogeny, suggesting horizontal transmission events between drosophilids and even between drosophilids and species of other families, subfamilies and orders. Moreover, some sequences present open reading frames, conserved catalytic motifs and evidence for the action of a strong purifying selection, which suggest yhat they originated from active elements. In another part of the work, we characterize Paris-like elements (belonging to Tc1 family), through searches in the twelve Drosophila genomes available. These searches, enabled us to find five new Paris-like elements (one in D. ananassae, one in D. pseudoobscura, one in D. persimilis, one in D. mojavensis and one in D. willistoni), with a copy number ranging from two to seven. Three species have putatively active elements. The evolutionary analysis of these elements suggests that they have envolved through vertical transmission associated with some events of stochastic loss in the analysed species. / Elementos transponíveis (TEs) são regiões do DNA que podem se mover dentro e entre genomas, causando grande impacto na evolução dos organismos. A Superfamília Tc1-Mariner se destaca por ser, provavelmente, a superfamília de transposons de DNA com maior distribuição na natureza, sendo ubíqua em eucariotos. Em parte desse trabalho, caracterizamos elementos da família mariner em drosofilideos Neotropicais para os quais obtivemos amplificação com primers degenerados. Os primers foram construídos na região do domínio catalítico da transposase de mariner o que permite amplificar uma ampla gama de sequências relacionadas à mariner. Um total de 23 espécies apresentou sequências relacionadas à mariner pertencentes a três subfamílias (mellifera, mauritiana e irritans). Esses elementos apresentaram uma distribuição descontínua e incongruências com a filogenia das espécies hospedeiras, o que sugere eventos de transmissão horizontal entre drosofilideos e, até mesmo entre drosofilideos e espécies de outra família, superfamília e ordem. Além disso, algumas sequências apresentaram um quadro aberto de leitura, os motivos catalíticos conservados e uma forte seleção purificadora atuando, o que sugere que esses elementos sejam provenientes de elementos ativos. Em outra parte do trabalho, caracterizamos as sequências relacionadas ao elemento Paris (pertencentes à família Tc1), com buscas nos doze genomas de Drosophila disponíveis. Nessas buscas,foram encontrados cinco novos elementos relacionados à Paris (um em D. ananassae, um em D. pseudoobscura, um em D. persimilis, um em D. mojavensis e um em D. willistoni), com um número de cópias variando de dois a sete. Três espécies apresentaram elementos potencialmente ativos. A análise evolutiva desses elementos sugere que estão sendo mantidos por transmissão vertical, com alguns eventos de perda estocástica nas espécies analisadas.

Das Neuroblastom ist der dritthäufigste maligne Tumor im Kindesalter und ist für 15% der Todesfälle durch Krebs bei Kindern unter 14 Jahren verantwortlich. Viele molekularbiologische Vorgänge, die zu der heterogenen Prognose der Patienten beitragen, sind noch nicht verstanden. Als Hauptrisikomerkmal stellt sich die Amplifikation und erhöhte Expression von MYCN dar. In Vorarbeiten der Arbeitsgruppe von Prof. Christiansen zeigte MYCN Einfluss auf die Genregion von Thyroid Cancer 1 (TC1), das als neuer Marker für maligne Schilddrüsenkarzinome erkannt wurde. In der vorliegenden Arbeit wurden erste Untersuchungen zur prognostischen Bedeutung von TC1 im Neuroblastom, sowie die Charakterisierung eines TC1 Überexpressionsphänotyps humaner Neuroblastomzelllinien unter Einfluss von MYCN durchgeführt. Es wurde ein Überexpressionsvektor von TC1 in die Neuroblastomzelllinie SH-EP eingebracht, welche über ein aktivierbares MYCN- Konstrukt verfügt. Dieser neue Phänotyp wurde bezüglich der Proliferation, des Zellzyklus und der Apoptose im Vergleich zu einer Kontrollzelllinie ohne Überexpression untersucht. Eine In-silico Recherche in der Versteeg Neuroblastomdatenbank ergab eine deutlich bessere Überlebenswahrscheinlichkeit für Patientin mit hoher TC1 Expression. Es konnte gezeigt werden, dass MYCN Amplifikation und Expression in einem Panel von Neuroblastom Zelllinien nicht mit der TC1 Expression korrelieren. Die spezifische Aktivierung von MYCN führte hingegen zu einer Expressionssteigerung von TC1. Weiterhin zeigte sich, dass eine TC1 Überexpression die Proliferation hemmt, indem es die MYCN induzierte G1- S- Phasen- Transition inhibiert. TC1 zeigt antiproliferative Eigenschaften im Zellkulturmodell und stellt sich als neuer prognostisch günstiger Parameter im Neuroblastom dar.

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 Stowaway MITEs are mobilized by transposases from the Tc1/Mariner superfamily of TEs. To retrieve all Tc1/Mariner TEs from the genome, bioinformatic approaches were performed. A total of 295 Tc1/Mariner TEs that encoded a full or partial transposase were recorded which 100 were newly described. Sequence alignment, and identification of the catalytic motif placed these transposases into eight groups. A functional link was established by comparing the terminal sequences of the Stowaway-like MITEs to the termini of the terminal sequences of Tc1/Mariner TEs. A yeast excision assay was used to experimentally test these functional links. Majority of the Stowaway-like MITE and transposase combinations tested did not indicate a functional link. However, a possible functional link was observed between the AATp3-13 transposase and AAStow-5 Stowaway-like MITEs.

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 Stowaway MITEs are mobilized by transposases from the Tc1/Mariner superfamily of TEs. To retrieve all Tc1/Mariner TEs from the genome, bioinformatic approaches were performed. A total of 295 Tc1/Mariner TEs that encoded a full or partial transposase were recorded which 100 were newly described. Sequence alignment, and identification of the catalytic motif placed these transposases into eight groups. A functional link was established by comparing the terminal sequences of the Stowaway-like MITEs to the termini of the terminal sequences of Tc1/Mariner TEs. A yeast excision assay was used to experimentally test these functional links. Majority of the Stowaway-like MITE and transposase combinations tested did not indicate a functional link. However, a possible functional link was observed between the AATp3-13 transposase and AAStow-5 Stowaway-like MITEs.

Submitted by Anderson Silva (avargas@icict.fiocruz.br) on 2012-03-23T18:08:27Z No. of bitstreams: 1 lauren_h_jaeger_ioc_mt_0003_2010.pdf: 980575 bytes, checksum: 58e8d10d1a1194b26a55ff028cdccc2e (MD5) / Made available in DSpace on 2012-03-23T18:08:27Z (GMT). No. of bitstreams: 1 lauren_h_jaeger_ioc_mt_0003_2010.pdf: 980575 bytes, checksum: 58e8d10d1a1194b26a55ff028cdccc2e (MD5) Previous issue date: 2010 / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil / Trypanosoma cruzi (T. cruzi) é o agente causador da doença de Chagas, que afeta entre 8 e 9 milhões de pessoas em todo mundo. Este protozoário é responsável por uma variedade de manifestações clínicas em humanos, possui uma ampla gama de hospedeiros e apresenta grande diversidade genética e biológica. As pequenas regiões codificantes (uORFs) presentes na região 5’não traduzida (5’UTR) de mRNAs maduros são conhecidas por afetar a eficiência da tradução de muitos genes eucariotos. Pouco é conhecido sobre a existência e conservação de uORFs em genes de Tripanossomatídeos. Este trabalho se propôs avaliar o grau de conservação das uORFs e seu potencial como marcador molecular das populações de T. cruzi, através da análise de sete genes contendo uORFs previamente selecionados. Oligonucleotídeos iniciadores foram desenhados e fragmentos das 5’UTRs contendo uORFs foram amplificados, através de PCR, de cepas representativas de cada um dos três grupos populacionais do parasito, TcI, TcII e ZIII. Após clonagem e sequenciamento, alto grau de conservação das uORFs foi observado de um ponto de vista populacional e a ruptura de uma uORF foi observada em apenas um gene. Isto é um forte indicativo de que em T. cruzi essas uORFs são funcionalmente ativas, pois do contrário teriam sido extintas das 5’UTRs durante o processo evolutivo sofrido pelos grupos populacionais de T. cruzi. A observação de mutações grupo-específicas nas sequências nucleotídicas das 5’UTRs de alguns genes, motivou a realização de testes para a utilização desses fragmentos como possíveis marcadores moleculares para as populações do parasito. A obtenção dos fragmentos dos genes codificantes de ATPase e Ferredoxina foi realizada em mais de 15 cepas e isolados. Verificou-se a existência de mutações grupo-específicas na 5’UTR do gene ATPase, que corroboram com a classificação filogenética proposta deste parasito. Na 5’UTR do gene Ferredoxina, notou-se a presença de uma sequência repetitiva simples, composta por dinucleotídeos CA (citosina e adenina) seguidos de mononucleotídeos A. As variações desta repetição puderam ser utilizadas para agrupar todos os isolados/cepas de T. cruzi do estudo em nove genótipos distintos, os quais são relativamente independentes da classificação atualmente proposta de três grandes grupos populacionais. O uso desta pequena repetição na 5’UTR do gene Ferredoxina permite uma nova forma de classificar os isolados e cepas de T. cruzi. / Trypanosoma cruzi is the causative agent of Chagas disease in humans, and affects about nine million of people around the world. It induces a variety of clinical presentations in patients, have a wide range of vertebrate hosts and exhibits great diversity of genetic and biological characteristics. Upstream Open Reading Frames (uORFs) are small open reading frames located in the 5’ UTR of a mature mRNA. They have been shown to affect the translation efficiency of many eukaryotic genes. Scarce information is available about the existence and conservation of uORFs in Trypanosomatids genes. This study aims to evaluate both the degree of sequence conservation in uORFs and its potential as molecular marker of populations of T. cruzi. To this end, upon a PCR amplification and cloning of 5'UTR fragments, sequence analysis of seven genes that presents uORFs were carried out in four strains that are typical representative of three main population groups in T. cruzi. A remarkable degree of conservation of uORFs was observed in all isolates. Out of several mutational events observed in these uORFs, a disruption of a uORF was observed in only one gene. This indicates that in T. cruzi these uORFs are functionally active, otherwise it would have changed during the evolutionary process. The observation of group-specific mutations in the 5'UTRs of some genes suggested that they could be used in an PCR amplification assay as molecular markers for T. cruzi populations. The fragments of genes ATPase and Ferredoxin were amplified from 15 strains and isolates. After sequencing, the group-specific mutations observed in the 5'UTR of the gene ATPase corroborate the current classification of T. cruzi populations in three main groups: TcI, TcII and ZIII. In the 5'UTR of the Ferredoxin gene, the sequence alignment revealed the presence of a small repetitive sequence composed of dinucleotides CA and mononucleotides Adenine. The variations in length and composition of this simple repetitive sequence allowed the clustering of all 15 isolates into nine distinct genotypes, which were not correlated to main population groups. Thus, a new approach to strain typing in T. cruzi can be envisaged by using this SSR (simple sequence repeat).

Transposable elements (TEs) are mobile genetic elements capable of replicating and spreading within, and in some cases, between genomes. I describe a whole-genome analysis of DD34E TEs, which belong to the IS630-Tc1-mariner superfamily of DNA transposable elements, in the African malaria mosquito, Anopheles gambiae. Twenty-six new transposons as well as a new family, gambol, were identified. The gambol family shares the DD34E catalytic motif with Tc1-DD34E transposons, but is distinct from these elements in their phylogenetic relationships. Although gambol appears to be related to a few DD34E transposons from cyanobacteria and fungi, no gambol elements have been reported in any other insects or animals thus far. This discovery expands the already expansive diversity of the IS630-Tc1-mariner TEs, and raises interesting questions as to the origin of gambol elements and their apparent diversity in An. gambiae. Several DD34E transposons discovered in An. gambiae possess characteristics that are associated with recent transposition, such as high sequence identity between copies, and intact terminal-inverted repeats and open reading frames. One such element, AgTango, was also found in a distantly related mosquito species, Aedes aegypti, at high amino acid sequence identity (79.9%). It was discovered that Tango transposons have patchy distribution among twelve mosquito species surveyed using PCR as well as genomic searches, suggesting a possible case for horizontal transfer. Additionally, it was discovered that in some mosquito genomes, there are several Tango transposons. These observations suggest differential evolutionary scenarios and/or TE-host interaction of Tango elements between mosquito species. This strengthened the case that AgTango may be a functional transposase, and I sought to test its potential activity in a cell culture-based inter-plasmid transposition assay using the Herves plasmids as a positive control (Arensburger et al., 2005). AgTango constructs were successfully constructed; however, no transposition events were detected for Tango or Herves. Because the positive control failed to work, no assessment can be made concerning Tango's transposase. Possible causes and solutions for these results, alternative means to detect transposition, as well as future directions with Tango are discussed. / Ph. D.

Transposons sind genetische Elemente, die fähig sind, sich innerhalb des Genoms zu bewegen. Sleeping Beauty (SB) gehört zur Tc1/mariner-Superfamilie von Transposons. SB wurde aus molekularen Fossilien rekonstruiert um u.a. einen sicheren und effizienten Vektor für die Gentherapie zu schaffen. Zu diesem Zweck ist es notwendig, den Mechanismus der SB-Transposition und deren Regulation, die Aktivitäten des Proteins und den Einfluss von Wirtsfaktoren genau zu verstehen. In meiner Arbeit habe ich die einzelnen Schritte des Transpositionsprozesses und die Bildung des sogenannten paired-end complex (PEC) – eine Voraussetzung für die folgenden katalytischen Reaktionen – untersucht. Zusätzlich habe ich versucht, einen in vitro Transpositionstest für SB zu etablieren. SB gehört zur IR/DR-Gruppe der Tc1/mariner-Superfamilie. Im Gegensatz zu mariner-like-Elementen ist die IR/DR-Struktur von SB durch lange IRs mit insgesamt vier Bindestellen für die Transposase gekennzeichnet. Ich habe die Fähigkeit dieser beiden Transposon-Systeme zum Ausschneiden eines Transposonendes ohne die Beteiligung des anderen Endes im PEC getestet. Solche unpräzise Transposition kann zu genomic rearrangements führen. Meine Ergebnisse zeigen, dass SB zwar imstande ist, ein einzelnes Transposonende auszuschneiden, dies geschieht jedoch weit weniger effizient als bei mariner-like-Elementen. Die Unterdrückung unpräziser Transpositionsereignisse ist ein Ergebnis der besseren durch die IR/DR-Struktur bedingten Regulation von SBs Transposition. Die Komplexität der IRs in Kombination mit der zweiteiligen DNA-Bindedomäne von SB kann als Mittel einer raffinierten Regulation des Transpositionsprozesses angesehen werden, welche das Genom vor anormalen Transpositionsereignissen schützt. Die Ergebnisse meiner Arbeit legen ein Modell nahe, in dem die Bildung des PEC während der Transposition von SB ein höchst genau regulierter Prozess ist, der durch die DNA-Protein- und Protein-Protein-Bindeaffinitäten geleitet wird. / Transposons are pieces of DNA able to move within the genomes. Sleeping Beauty is a verterbrate Tc1/mariner transposon reconstructed from molecular fossils to create a safe and efficient vector for gene therapy. For that purpose it is important to deeply understand the mechanism and regulation of the SB transposition, the activities of the transposase and influence of host factors on the process. Therefore, in this project I studied the single steps of the transposition reaction and formation of the paired-end complex (PEC) which is a prerequisite for the subsequent catalytic steps. Additionally, I tried to establish an in vitro transposition assay for Sleeping Beauty that would serve an easy assay for testing the system and probe mechanisms affecting the regulation of transposition activity. Sleeping Beauty belongs to the IR/DR subfamily of the Tc1/mariner-like transposons. In contrast to mariner-like elements the IR/DR structure of SB is characterized by long IRs with four binding sites for the transposase. I compared the ability of the two systems to perform cleavage of the single transposon end without including the second end in the PEC. Such imprecise transposition can lead to genome rearrangements. My results show that SB is capable of single-end cleavage; however, to much lower extent than the mariner-like element. Lower number of imprecise transposition events is a result of better regulation of the SB transposition imposed by the IR/DR stucture. The complexity of the inverted repeats together with the bipartite DNA-binding domain of SB might offer means for more sophisticated regulation of the transposition process, thereby protecting the genome from aberrant transposition events. I propose that complex formation in SB transposition is a strictly regulated ordered assembly process, guided by DNA-protein and protein-protein interaction interfaces of the DNA-binding subdomains. Obtained results allowed me to draw a model how the paired-end complex is formed.

Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19