Retrotransposon mobilization is a major source of genome evolution. However, the functional consequences of these events, and particularly their influence upon transcriptional activity, are poorly defined. The extent of retrotransposon transcription, as well as that of other repetitive elements, has eluded systematic study due to difficulties in discriminating elements copied in multiple genomic loci. Moreover, the potential regulatory effects of retrotransposon transcription upon the expression of neighbouring protein-coding genes are also largely unknown. This thesis develops methods to survey repetitive element expression and assess the functions of retrotransposons in the mouse and human genomes. Chapter 1 summarises the complex transcriptional output of the mammalian genome, the functional annotation of this expression and the genomic and bioinformatic tools available for its detection. Chapter 2 explores the capacity of short sequence tags to discern transcription from individual repetitive elements, as well as from protein-coding genes. It is based upon a publication that critiqued the bioinformatics associated with Cap Analysis Gene Expression (CAGE) and developed novel methodologies to resolve repetitive element transcription. Chapter 3 describes the development of an updated CAGE mapping pipeline for the fourth stage of the international Functional Annotation of Mouse (FANTOM) project, which lead to the generation of a research article and a book chapter. These works demonstrated the enhanced utility of CAGE when coupled with next-generation sequencing, highlighted the benefits of CAGE when applied to systems biology and profiled the temporal expression of human repetitive elements. Chapter 4 presents an in-depth analysis of repetitive element transcription in the mouse and human genomes. Using CAGE, approximately 250,000 retrotransposon associated transcription start sites were defined, many of which were tissue-specific. Retrotransposons were found to frequently function as alternative promoters for protein-coding genes and/or express non-coding RNAs. Furthermore, when retrotransposons were found within the 3’UTR of protein-coding genes, there was strong evidence for the reduced expression of the corresponding transcripts. A genome-wide screen for strong expression correlation between repetitive elements and neighbouring protein-coding genes identified approximately 23,000 candidate regulatory regions derived from retrotransposons, including several hundred putative boundary elements. These were in addition to more than two thousand examples of bidirectional transcription found in retrotransposons, which are known to be a source of double stranded RNAs involved in RNA interference. Chapter 5 explores the proportion of the mouse embryonic stem cell transcriptome comprised of repeat-derived transcripts, using next-generation RNA sequencing. This study defined the dynamic expression of repetitive elements at the greatest resolution achieved to date and demonstrated that repetitive elements are an intrinsic part of the mammalian transcriptional landscape.

Orientador: Cesar Martins / Banca: Luciana Bolsoni / Banca: Maeli Del Paiva / Resumo: O genoma dos organismos eucariotos apresenta-se organizado em seqüências simples e repetidas. As seqüências repetidas de DNA estão presentes em centenas a milhares de cópias dispersas ou agrupadas no genoma e localizam-se preferencialmente em regiões heterocromáticas, desempenhando papel relevante na organização do genoma desses organismos. Nesse sentido, a realização de estudos genéticos básicos sobre a organização genômica dessas seqüências repetidas é fundamental para uma melhor compreensão do seu papel biológico assim como o entendimento de sua dinâmica evolutiva entre os diversos grupos de vertebrados. Os Cichlidae constituem uma das mais especiosas famílias de peixes, com cerca de 3.000 espécies distribuídas pela América Central e do Sul, África, e sudeste da Índia. Este grupo passou por um rápido e extenso processo de radiação adaptativa ao longo dos tempos, constituindo-se em importantes entidades biológicas para a realização de estudos evolutivos. Dentre os Cichlidae, as espécies do gênero Cichla (tucunarés), com distribuição exclusiva na América do Sul, apresentam grande importância ecológica e econômica. No entanto, estudos genéticos envolvendo espécies desse gênero são ainda escassos. Assim, o presente trabalho teve por objetivo isolar e caracterizar seqüências repetidas de DNA no genoma de Cichla kelberi. Elementos repetidos de DNA foram isolados por PCR (elementos Rex1, Rex3, Rex6 e Tc1) e digestão enzimática (elemento Tuc), seqüenciados e mapeados cromossomicamente por FISH para o estudo de seu padrão de distribuição no genoma. O elemento Tuc apresentou elevada similaridade com seqüências do gene da transcriptase reversa de Oryzias melastigma, o que sugere tratar-se de um elemento retrotransponível. Análises comparativas do elemento Tuc a bancos de sequência mostraram alta similaridade... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The genome of eucaryote organisms is organized into single and repetitive sequences. The repetitive DNA sequences are represented by hundreds to thousands of dispersed or tandem-arrayed copies preferentially localized on the heterochromatic regions, having important function on the genome organization of the organisms. Therefore, the development of basic genetic studies about the genome organization of these repetitive sequences are fundamental to a better comprehension of their biologic role and the understanding of their evolutionary dinamics. The Cichlidae are one of the most diverse fish families, having about 3.000 species distributed around Central and South America, Africa and Southeast India. This group underwent a large and rapid process of adaptative radiation, becoming an important biological model. Among the Cichlidae, the species of the genera Cichla (tucunarés), with exclusive distribution in South America, have a significative economic and ecologic importance. However genetic studies on species of this genera are scarce. Therefore, this work had the aim to isolate and characterize repetitive DNA sequences of the genome of Cichla kelberi. Repetitive DNA sequences were isolated using PCR (elements Rex1, Rex3, Rex6 and Tc1) and restriction digestion (element Tuc), sequenced and their genome distribution determined by FISH. The Tuc element showed high similarity to sequences of reverse transcriptase gene of the fish Oryzias melastigma, which suggests that such element correspond to an retrotransposon element. Comparative analysis of the Tuc element to DNA sequence data bank showed high similarity with repetitive sequences in the genome of several vertebrates, including fishes, amphibians and mammals. Results of FISH showed an accumulation of obtained elements preferentially in centromeres of all chromosomes of the complement, and few telomeric blocks in some... (Complete abstract click electronic access below) / Mestre

The maintenance of genomic stability through suppression of retrotransposon activity is vital for the avoidance of potentially mutagenic genomic disruption caused by retrotransposition. Germline development is a particularly important phase for retrotransposon silencing as retrotransposition events here have the potential for transmission to the entire embryo, threatening the health of offspring. A collection of germline genome defence genes are required for the suppression of retrotransposons in the developing germline of male mice (e.g. Tex19.1, Dazl, Mili, Miwi2, Gasz, Mov10l1, Mael, Dnmt3l), all of which trigger meiotic prophase arrest when mutated. I have analysed the meiotic defects which arise in Tex19.1-/- male mice to contribute to the understanding of the fundamental mechanisms required for successful completion of meiosis and to investigate the involvement of retrotransposon silencing in this process. The absence of TEX19.1 in male mice causes infertility; with failed chromosome synapsis in ~50% of pachytene nuclei and associated apoptosis, as well as individual univalent chromosomes in 67% of remaining nuclei progressing to metaphase I. Where studied, failed chromosome synapsis is a common feature of germline genome defence mutant spermatocytes. One aim of my studies has been to better understand the mechanism responsible for this failed chromosome synapsis. I have demonstrated that unlike Mael-/- spermatocytes, additional SPO11-independent DNA damage potentially attributable to retrotransposition is not detectable in Tex19.1-/- spermatocytes. Rather, the formation of meiotic DNA double strand breaks (DSBs) is dramatically reduced in early prophase to around 50%, resulting in a reduction in nuclear γH2AX signal, production of SPO11- oligonucleotide complexes and foci formation by early recombination proteins RPA, DMC1 and RAD51. Despite this early reduction, DSB frequency recovers to more normal levels shortly after in zygotene. I have shown that defective pairing of homologous chromosomes by meiotic recombination is likely responsible for the asynapsis previously reported. The initial reduction in DSB frequency could be sufficient to cause failed chromosome synapsis in this mutant, assuming that late-forming DSBs cannot participate effectively in promoting homologous pairing. Alternative hypotheses include altered positioning of DSBs in response to altered chromatin organisation relating to retrotransposon upregulation, misguiding the pairing of homologous chromosomes. Such a model of disruption could also extend to other germline genome defence mutants. I have demonstrated that despite successful pairing of homologous chromosomes in a sub-population of Tex19.1-/- spermatocytes, subsequent progression of these cells through pachytene is delayed. Numerous diverse features of progression are all delayed, including recombination, ubiquitination on autosomes and sex chromosomes, expression of the mid-pachytene marker H1t, and chromosome organisation. The delay identified is related to recombination therefore this feature is likely to stem from the initial defect in DSB formation early in prophase. While some delayed features are probably directly related to recombination, others are not. The coordinated delay observed may suggest the presence of a recombination-sensitive cell-cycle checkpoint operating to regulate progression through pachytene. My research has also aimed to establish the cause of elevated univalent chromosomes not connected by chiasmata in metaphase I Tex19.1-/- spermatocytes. I have demonstrated that that absence of chiasmata is not due to failed crossover formation between synapsed chromosomes. Rather, the frequent observation of individual unsynapsed chromosomes during crossover formation suggests that some spermatocytes with low-level asynapsis are leaking through meiotic checkpoints and are unable to form a crossover before reaching metaphase. Therefore, again this later meiotic defect appears to stem from the initial defect in meiotic DSB formation, the consequences of which vary widely in severity. Remarkably the unsynapsed chromosomes present during crossover formation include both sex chromosomes, and autosomes. Tolerance of an unsynapsed autosome from pachytene into metaphase is an unusual observation in mice and this observation may aid the understanding of spermato cyte quality control mechanisms during this progression. Together these findings have greatly advanced the understanding of the infertility incurred during meiosis in Tex19.1-/- male mice. These findings may also extend to benefit the understanding of other germline genome defence mutants. Diverse observations made during my investigations also reveal a potential system of coordinated progression through pachytene relating to meiotic recombination. The variable severity of the synapsis defects incurred in this mutant appears to have variable effects on spermatocyte survival and could also inform the understanding of meiotic checkpoint sensitivity.

Long terminal repeat (LTR) retrotransposons account for approximately 10% of mouse and 8% of human genomes and may play a role in modifying gene expression. Many species harbor retrotransposon families encompassing both autonomous and non-autonomous members. Specifically, the mouse Early Transposon (ETn) family members lack all retroviral genes but are transcriptionally and retrotranspositionally active, causing over 20 known insertional germline mutations. ETns owe their retrotransposition potential to proteins encoded by structurally intact MusD retrotransposons with whom they share LTRs. ETn elements are transcribed at a much higher level than MusD retrotransposons in embryos and undifferentiated cells, suggesting their evasion of host restriction mechanisms. However, mechanisms responsible for the replicative success of non-autonomous retrotransposon subfamilies over their coding-competent relatives are poorly understood. In the first stage of my research, I analyzed regulatory sequences in an ETn LTR responsible for its high promoter activity in the undifferentiated cell line P19. I found that three GC-boxes that may function as Sp1/Sp3 binding sites act synergistically and are indispensable for undifferentiated cell-specific promoter activity of the LTR. Sp1 binding partners may be responsible for the restricted ETn expression. Moreover, I have shown that unlike many retroviruses, ETn elements possess multiple transcription initiation sites and that they have amplified via intracellular retrotransposition in the P19 teratocarcinoma cell line. In the next step of my research, I performed analysis of epigenetic mechanisms as a means of ERV suppression. Specifically, I showed that in embryonic stem cells, autonomous MusD retrotransposons are epigenetically suppressed to a greater degree than non-autonomous ETn retrotransposons, illustrated by a higher level of DNA methylation and a lower level of active histone modifications. I hypothesize that MusD elements may be silenced by DNA methylation and repressive chromatin spreading into the LTR from the CpG-rich internal retroviral sequence absent in ETn elements. I propose that internal structure largely devoid of high CG content enables ETn elements to evade host-imposed transcriptional repression, contributing to their high mutagenic activity in the mouse germline. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

[EN] Citrus is a diverse genus within the Aurantioideae subfamily that comprises an undetermined number of pure species natively found in a vast territory extending from India to Japan and Australia. Besides pure species, countless citrus admixtures of commercial interest such as mandarins, oranges and lemons have been traditionally included in this genus, even though they are the product of several interspecific crosses between pure species. Recently, a genome-wide analysis provided the backbone of the Citrus phylogeny, showing that the wild species diverged from an ancestral citrus in a rapid radiation during the Late Miocene. Understanding the processes that shaped the evolution and domestication of the genus will provide novel insights in the field of plant genome evolution. In this doctoral thesis, multiple genomic approaches have been used to expand the existing knowledge on major determinants driving the processes of evolution, diversification and domestication in Citrus. First, a genome-wide Aurantioideae phylogeny was generated, revealing the existence of several independent dispersal events in this subfamily in the last 10 million years, from Asia to Africa and Australia, and rooting the Citrus genus within this subfamily. The Citrus phylogeny was then studied under the multispecies coalescent model, which can capture the variability generated during fast radiations. The dating of the speciation events allowed to advance original proposals on the paleogeographic events triggering the migration of the Citrus species through the South East Asian region. The Citrus radiation generated the great genetic and phenotypic diversity found in this genus. To investigate the effects of the Late Miocene climate change on the genomic structure of the Citrus pure species, the activity and evolution of retrotransposons, which can significantly alter the genome of their hosts, was analyzed. Most of the Citrus retrotransposon families are shared with Severinia buxifolia, an Aurantioideae species that diverged from Citrus more than 10 million years ago, implying that few retrotransposon families are specific to the genus Citrus. However, estimations of the retrotransposon insertion rates within Citrus revealed that, shortly after the radiation, the transposon activity rapidly changed among the different species. Hence, the data indicates that retrotransposon dynamics are linked to the stress caused by the Late Miocene climate change and the Citrus speciation, although specific responses likely depend on the particular evolutionary history of each species. The differences of gene expression in fruits of domesticated and wild cultivars were then studied to understand the role of interspecific hybridizations during Citrus domestication. The results presented suggest that these events, together with asexual propagation, were key for the domestication process. Different mechanisms explaining commercially relevant Citrus traits are also proposed. For example, pulp acidity in citrons and lemons is linked to an increased proton influx to the pulp vacuoles. The data also indicate that the peel pigmentation might be controlled by the additive effect of several minor genes, and not by a single gene or mechanism. Finally, an allele-dependent expression pattern of a chalcone synthase, involved in the flavonoid biosynthesis, advocates for the existence of a stepwise evolution in the mandarin flavonoid accumulation. All in all, the transcriptomic approach used in this work allowed to generate broader hypotheses that stand from a genus-wide perspective. Overall, the results provide a comprehensive framework of Citrus phylogenetic relationships, the effect of the mobile elements during its diversification and the role of interspecific hybridizations in the citrus domestication. The insights here exposed reveal the inherent complexity of the evolutionary history of this fascinating genus. / [ES] El género Citrus (Aurantioideae) abarca un número desconocido de especies puras, nativas en buena parte del sudeste asiático y Oceanía. Muchas variedades comerciales, como mandarinas o naranjas, también forman parte de este género. Recientemente, la estructura de la filogenia del género Citrus ha sido publicada en un estudio el que se propone que los cítricos actuales surgieron en un proceso de radiación rápida durante el Mioceno tardío, hace 8 millones de años. Una mejor comprensión de los procesos involucrados en la evolución y posterior domesticación del género Citrus proporcionaría nuevas perspectivas en el ámbito de la genómica de plantas. En esta Tesis Doctoral se han empleado diversas estrategias genómicas para ampliar el conocimiento existente sobre los procesos implicados en la evolución, diversificación y domesticación de los cítricos. En primer lugar, se generó un árbol filogenético de las Aurantioideae, anclando el género Citrus dentro esta subfamilia. Esta filogenia reveló varios eventos de dispersión entre estas especies, generalmente desde Asia hacia África u Oceanía. Después, se estudió la filogenia del género Citrus empleando el modelo coalescente de multiespecie, que refleja la variabilidad inherente a los procesos de radiación. La datación de los distintos eventos de especiación ha permitido hacer nuevas propuestas sobre la paleogeografía y su papel en la distribución actual de los cítricos a lo largo del sudeste asiático. Para investigar los efectos del cambio climático del Mioceno tardío en el genoma de los cítricos, se analizó la actividad y la evolución de los retrotransposones como fuente de variabilidad genética en distintas especies de cítricos. Muchos de los retrotransposones de los cítricos también se encuentran en Severinia¿ un género de las aurantioideas que divergió del ancestro de los cítricos hace 10 millones de años, sugiriendo que pocos de los retrotransposones de cítricos son exclusivos de este género. En cambio, las tasas de inserción de retrotransposones en cítricos revelaron que la actividad de estos elementos cambió drásticamente entre especies poco después de la radiación de los cítricos. Por tanto, es posible que dicha actividad esté ligada al estrés climático durante el Mioceno tardío, así como a la especiación de los cítricos, aunque también parece verse afectada por las condiciones evolutivas particulares de las especies estudiadas. Por último, se estudiaron las diferencias en la expresión génica entre variedades domesticadas y especies salvajes para conocer el papel de las hibridaciones interespecíficas en la domesticación de los cítricos. Los resultados obtenidos sugieren que dichas hibridaciones, junto a la propagación clonal, fueron clave para el proceso de domesticación. Estos resultados también permiten proponer un mecanismo que explica la acidez de la pulpa de cidros y limones basado en el flujo de protones al lumen vacuolar. Los datos también parecen indicar que el color de los cítricos no depende de un único gen, sino que depende del efecto aditivo de varios genes en conjunto. Finalmente, se descubrió una copia del gen de la chalcona sintasa, necesario para la síntesis de flavonoides, que tan solo se expresa en mandarinas y variedades derivadas, lo que sugiere que la acumulación de flavonoides en estas variedades proviene de un proceso evolutivo escalonado. La obtención de estos resultados fue posible gracias a la estrategia de análisis transcriptómico escogida, que abarca varias especies del género Citrus. En conclusión, los resultados presentados en este trabajo aportan un marco de trabajo global en la filogenia del género Citrus, además de realizar nuevas propuestas sobre el efecto de los elementos móviles en la diversificación de los cítricos y el papel de las hibridaciones interespecíficas durante su domesticación. Los datos presentados en este trabajo revelan la compl / [CAT] El gènere Citrus (Aurantioideae) comprèn un nombre desconegut d'espècies pures, natives en un ampli territori que s'estén pel sud-est asiàtic i Oceania. Un gran nombre de varietats comercials de cítrics, com mandarines, taronges o llimes, també s'inclouen dins del gènere Citrus. L'estructura bàsica de la filogènia del gènere Citrus ha sigut publicada recentment, a un estudi al que es proposa que els cítrics actuals sorgiren en un procés de radiació ràpida que va tindre lloc en el Miocè superior, fa 8 milions d'anys. Una millor comprensió dels processos involucrats en l'evolució i posterior domesticació del gènere Citrus podria proporcionar noves perspectives dins de l'àmbit de l'evolució del genoma de plantes. Al llarg d'aquesta Tesi Doctoral s'han emprat diverses estratègies genòmiques per a ampliar el coneixement existent sobre els processos que van dirigir l'evolució, diversificació i domesticació dels cítrics. En primer lloc, es va generar una filogènia de les aurantioideas, ancorant el gènere Citrus dins d'aquesta subfamília. Esta filogènia va revelar l'existència de diversos esdeveniments de dispersió en estes espècies, generalment des d'Àsia cap a Àfrica o Oceania. Després, la filogènia dels cítrics es va estudiar emprant el model evolutiu coalescent multiespècie, que reflecteix la variabilitat inherent als processos de radiació ràpida. La datació de la especiació dels cítrics han permès fer noves propostes sobre la paleografia i el seu paper en la distribució actual dels cítrics per tot el sud-est asiàtic. Per a investigar els efectes del canvi climàtic ocorregut durant el Miocè superior en l'estructura genòmica dels cítrics, s'analitzà l'activitat i evolució dels retrotransposons com a font de variabilitat genètica en distintes espècies de cítrics. La majoria dels retrotransposons dels cítrics també es troben en Severinia¿ un gènere de les aurantioidees que va divergir de l'avantpassat dels cítrics fa 10 milions d'anys, la qual cosa suggereix que tan sols unes poques famílies de retrotransposons son exclusives dels cítrics. En canvi, l'estimació de les taxes d'inserció dels retrotransposons revela que l'activitat d'aquests elements va patir canvis dràstics entre espècies poc després de la radiació dels cítrics. Per tant, l'esmenada activitat podria estar lligada a l'estrès climàtic de finals del Miocé, així com a l'especiació dels cítrics, encara que també sembla veure's afectada per les condicions evolutives particulars de cada espècie. Finalment, es van estudiar les diferències a l'expressió gènica entre varietats domesticades i espècies salvatges per a conèixer el paper de les hibridacions interespecífiques en el procés de domesticació dels cítrics. Els resultats suggereixen que aquestes hibridacions, junt a la propagació clonal de les varietats de interès, foren clau en la domesticació. Els resultats també han permès proposar un mecanisme que explica l'acidesa de la polpa de poncems i llimes basat en el flux de protons al lumen vacuolar. D'altra banda, el color dels cítrics no pareix dependre d'un únic gen, sinó de l'efecte additiu de diversos gens en conjunt. Finalment, s'ha trobat una còpia del gen de la chalcona sintasa, necessària per a la síntesi de flavonoides, que tan sols s'expressa en mandarines i varietats derivades, suggerint que l'acumulació de flavonoides en aquestes varietats és el resultat d'un procés evolutiu escalonat. L'obtenció d'aquests resultats fou possible gràcies a l'estratègia d'anàlisi escollida, que inclou diverses espècies del gènere Citrus. En conclusió, els resultats presentats en aquest treball aporten un marc de treball global a la filogènia dels cítrics, a banda de permetre realitzar noves propostes sobre el efecte dels elements mòbils en la diversificació dels cítrics i el paper de les hibridacions interespecífiques durant la seua domesticació. Les dades presenta / Borredá Fernández, C. (2021). A genomic approach to the evolution, diversification and domestication of the genus Citrus [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/176003 / TESIS

Retrons are genetic elements encoding reverse transcriptase (RT) usually located on the chromosome of a wide variety of mostly Gram-negative bacteria. Here we describe a new retron, designated Ne144, found in the chromosome of the myxobacterium Nannocystis exedens. This element codes for a 515-amino-acid RT that is most closely related to those found in other myxobacterial retrons. The RT is responsible for the production of a small satellite DNA called msDNA. This msDNA is composed of a 144 base, single-stranded DNA that is linked to a 72 base single-stranded RNA. The RNA strand is joined to the 5′ end of the DNA chain via a 2′-5′ linkage that occurs from the 2′ position of an internal guanosine residue in the RNA. In addition to the retron element, the chromosome of N. exedens also contains several partial copies of the msDNA sequence as revealed by DNA hybridization experiments using msDNA as a probe. One of these partial copies was characterized from a chromosome restriction fragment and found to contain a sequence that matches the last 82 bases of the DNA strand and five bases of the RNA strand in msDNA-Ne144. This partial copy of msDNA is very likely a retrotransposed sequence that was generated by reverse transcription using an RNA (the primer-template RNA for msDNA) as a template and the 3′ end of a nick in the chromosome as a primer, followed by incorporation into an open reading frame. The presence of this truncated copy of msDNA is strong evidence of retrotransposition in N. exedens causing an alteration in the bacterial genome.

Die Gattung Beta gehört zur Familie der Chenopodiaceae und wird in die vier Sektionen Beta, Corollinae, Nanae und Procumbentes unterteilt, wobei die Zuckerrübe der Sektion Beta zugeordnet wird. Aus dem Genom der Zuckerrübe und verwandter Wildarten konnten bereits eine Vielzahl von repetitiven DNA-Familien kloniert und untersucht werden. Mit der monosomen Fragmentadditionslinie PRO1 stand eine Chromosomenmutante zur Verfügung, die neben den 18 B. vulgaris-Chromosomen ein Chromosomenfragment der Wildrübe Beta procumbens enthält. Da dieses als Minichromosom bezeichnete Fragment mitotische Stabilität aufweist, muss es ein funktionelles Centromer besitzen, das auch im genetischen Hintergrund von Beta vulgaris aktiv ist. Mit der Erstellung einer BAC (bacterial artifical chromosome)-Bank von PRO1 wurde die molekulare Charakterisierung von Ty3-gypsy-Retrotransposons eines einzelnen Wildrüben-Centromers möglich. Die für die Wildrübe Beta procumbens spezifischen Satellitenrepeats pTS5 und pTS4.1 dienten der Selektion von BACs aus der Centromer-Region des PRO1-Minichromosoms. Die Identifizierung eines unikalen genomischen Locus, mit einer Verschachtelung von zwei nicht homologen LTR-Retrotransposons, ermöglichte die gerichtete Isolation der LTR-Retrotransposons Beetle1 und Beetle2. Das Retrotransposon Beetle1 hat eine Gesamtlänge von 6736 bp und wird von LTR-Sequenzen begrenzt, die eine Länge von 1091 bp (5’-LTR) bzw. 1089 bp (3’-LTR) aufweisen. Das LTR-Retrotransposon Beetle2 weist mit 6690 bp eine ähnliche Gesamtlänge wie Beetle1 auf. Es wird von deutlich kürzeren LTR-Sequenzen mit einer Länge von 774 bp begrenzt. Aufgrund der Reihenfolge der Polyproteingene lassen sich Beetle1 und Beetle2 in die Gruppe der Ty3-gypsy-Retrotransposons (Metaviridae) einordnen. Beide Retrotransposon-Familien besitzen ein einziges offenes Leseraster (open reading frame; ORF) mit fusionierten gag- und pol-Genen. Datenbankrecherchen zeigten hohe Homologien von Beetle1 und Beetle2 mit den centromerischen Ty3-gypsy-Retrotransposons CRM aus Zea mays, CRR aus Oryza sativa und cereba aus Hordeum vulgare. Diese centromerischen Retrotransposons (CRs) sind in den Poaceae stark konserviert und stellen neben Satellitenrepeats eine hochabundante Sequenzklasse der Centromere der Süßgräser dar. Da sie im 3’-Bereich des gag-pol-Polyproteins eine Chromodomäne aufweisen, werden sie der eigenständigen Gruppe der Chromoviren zugeordnet. Chromodomänen sind zur Bindung von Proteinen und DNA befähigt und spielen eine wichtige Rolle in der Chromatin-Modifikation und der Bildung von Heterochromatin-Regionen. Beetle1 und Beetle2 besitzen Motive einer Chromodomäne, die vermutlich für eine gerichtete Transposition in die Centromer-Region verantwortlich ist. Neben der geringen Divergenz von Beetle1- und Beetle2-Sequenzen sowohl im Genom von Beta procumbens als auch in den anderen Arten der Sektion Procumbentes spricht auch das junge Alter von 100 000 bis 350 000 Jahren und die Transkriptionsaktivität für eine Einordnung dieser Ty3-gypsy-Retrotransposons in die Gruppe der Chromoviren. Sowohl die Southern-Hybridisierung als auch die Fluoreszenz-in situ-Hybridisierung zeigten, dass Beetle1 und Beetle2 nur für die Sektion Procumbentes spezifisch sind und dort in hoher Kopienzahl vorkommen. Untersuchungen mit methylierungssensitiven Restriktionsendonukleasen veranschaulichten den hohen Grad an Cytosin-Methylierung von Beetle1 und Beetle2.

Tnt1 is a transcriptionally active LTR-retrotransposon, present in over 600 copies in the Nicotiana tabacum genome. Under normal growth conditions, Tnt1 expression is limited to basal levels, but its expression is further induced under biotic and abiotic stresses. Transgenic tobacco plants (HP plants) expressing a Tnt1 reverse transcriptase hairpin were generated. These showed pleiotropic phenotypes such as cell death spots on the leaves and callose deposition and other severe abnormal development in aerial and underground portions. RNA sequencing of leaves with cell death spots revealed a rewiring of transcriptional regulatory networks related to stress responses exclusive to HPs. Among the positively modulated genes were ethylene synthesis and response cascade genes. The objective of the present work was to unravel the relation observed between Tnt1 and ethylene, generating a model. The results obtained suggest that HP seedlings and plants have increased ethylene synthesis when compared to the wildtype. Folding prediction of Tnt1 messenger RNA allowed the identification of ethylene-responsive sequences in putative stem loop locations. Thus it is possible that Tnt1 expression can produce small RNAs targeted to sequences present in the Tnt1 retrotransposon itself as well as at the promoter region of other ethylene responsive genes. Quantification of the expression of Tnt1 and ethylene related genes revealed \"phase opposition\" expression kinetics in the HPs, which led us to hypothesize that there might be an antagonistic relationship between the expression of Tnt1 and the expression of ethylene responsive genes involved in plant defense responses. Our findings suggest that Tnt1 could generate sRNAs that exerts transcriptional control over itself as well as other genes. Our model establishes a completely new biological role for a retrotransposon: Tnt1 would provide feedback control to ethylene-mediated gene regulation in tobacco defense responses, bringing the system back to a homeostatic condition and turning the defense responses down. / Tnt1 é um retrotransposon com LTR transcricionalmente ativo, e está presente em mais de 600 cópias no genoma de Nicotiana tabacum. Em condições normais de crescimento Tnt1 é expresso em níveis basais. No entanto, sua expressão é induzida pelo estímulo de estresses bióticos e abióticos. Plantas de tabaco transgênicas (chamadas de HP) expressando um grampo da transcriptase reversa de Tnt1 foram geradas. Estas apresentaram fenótipos como: pontos de morte celular e deposição de calose nas folhas e severas anomalias de desenvolvimento severas nas porções aérea e radicular das plantas. Sequenciamento de RNA de folhas com os pontos de morte celular revelou uma reorganização de redes de regulação transcricional relacionadas a resposta a estresses. Essas novas redes surgiram exclusivamente nas plantas HP. Entre os genes modulados positivamente estavam genes de síntese e de resposta ao etileno. O presente trabalho teve como objetivo elucidar a relação observada entre Tnt1 e o fitormônio etileno gerando um modelo de atuação. Os resultados obtidos permitiram demonstrar que plântulas e plantas HP adultas tem um aumento na síntese de etileno quando comparadas à selvagem. A predição do dobramento do RNA mensageiro de Tnt1 permitiu a identificação de sequências responsivas ao etileno localizadas em posição potencial para formar grampos. Desta forma, é possível que a expressão de Tnt1 leve à produção de pequenos RNAs que tem como alvo sequências responsivas a etileno presentes tanto no próprio elemento quanto em regiões promotoras de outros genes. A quantificação da expressão de Tnt1 versus genes relacionados ao etileno revelou um padrão em \"oposição de fase\" nas HPs, o que nos levou a hipotetizar que talvez ocorra uma relação antagonista entre a expressão de Tnt1 e a expressão de genes responsivos ao etileno envolvidos em respostas de defesa vegetais. Nossos resultados sugerem que Tnt1 pode gerar pequenos RNAs que exercem controle transcricional sobre Tnt1 e outros genes endógenos. Nosso modelo estabelece um novo papel biológico para um retrotransposon: Tnt1 agiria como um modulador da indução de genes mediada por etileno nas respostas de defesa de tabaco, trazendo o sistema de volta à condição homeostática e encerrando as respostas de defesa.

Made available in DSpace on 2017-07-21T20:00:01Z (GMT). No. of bitstreams: 1 Patricia Barbosa.pdf: 1571215 bytes, checksum: daac7b661ca93cbfd05ca0e7cda85213 (MD5) Previous issue date: 2013-02-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The most part of the eukaryote genomes is constituted for repetitive DNA or multiple copies DNA, which has already been considered as “junk”, may be associated to the heterochromatin. In this study three Astyanax scabripinnis populations from Pindamonhangaba and Guaratinguetá (SP, Brazil) rivers and stream and one population from Maringá (PR, Brazil) were analyzed about the nucleolar organizing region (NORs), As51 satellite DNA, 18S and 5S rDNA location. Moreover, repetitive sequences were isolated and mapped through Cot-1 technique, which showed homology with UnaL2, a LINE type retrotransposon. The fluorescent in situ hybridization (FISH), with the isolated built retrotransposon probe, evidenced disperse labeled and stronger in centromeric and telomeric chromosomes regions, co-located and interspersed with the 18S DNAr and As51, proven by the fiber-FISH technique. The B chromosome of those populations showed very conspicuous labeled with the LINE probe, also co-located with the As51 sequences. The NORs were actives in a single site of a homologue pair in all three populations, with no evidence that the transposable elements and repetitive DNA have influence in its regulation at the performed analyzes level. / A maior parte do genoma dos eucariotos é constituída por DNA repetitivo ou DNA de múltiplas cópias, o qual já foi considerado “lixo”, podendo estar associado à heterocromatina. Neste estudo foram analisadas três populações de Astyanax scabripinnis provenientes de rios e córregos de Pindamonhangaba e Guaratinguetá (SP, Brasil) e uma população da cidade de Maringá (PR, Brasil) quanto a localização das regiões organizadoras de nucléolo (RONs), DNA satélite As51, DNA ribossomal (DNAr) 18S e DNAr 5S. Ainda, foram isoladas e mapeadas sequências repetitivas por meio da técnica de Cot-1, que mostrou homologia com UnaL2, retrotransposon do tipo LINE. A hibridação in situ fluorescente (FISH), com sonda construída para o retrotransposon isolado, evidenciou marcações dispersas e mais concentradas em regiões centroméricas e teloméricas dos cromossomos, co-localizadas e interespaçadas com DNAr 18S e As51, comprovada pela técnica de fiber-FISH. O cromossomo B das populações mostrou marcações bastante conspícuas com a sonda LINE, também co-localizada com sequências As51. As RONs apresentaram-se ativas em sítios únicos de um par homólogo nas três populações, não havendo indícios de que elementos transponíveis e DNA repetitivo tenham influência na sua regulação ao nível das análises realizadas.

Made available in DSpace on 2015-03-26T13:51:50Z (GMT). No. of bitstreams: 1 texto completo.pdf: 474764 bytes, checksum: dc1db5661d6bff9e0de8af890d4b1836 (MD5) Previous issue date: 2009-07-24 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Gypsy/Ty3 group retrotransposons are the main transposable elements found in the genome of pathogenic fungi. In this work, two retrotransposons termed MpSaci and Sophie were analyzed in Moniliophthora perniciosa and Cochliobolus heterostrophus, respectively. MpSaci was used to assess molecular markers based on transposable elements IRAP and REMAP. When 70 isolates of M. perniciosa were analyzed, a total of 43 loci were amplified by generating 46.51% polymorphism. Significant differences were found between populations of M. perniciosa divided in relation to biotope and the geographical origin, showing that populations are structured on the geographical origin and the host (biotype). The cluster analysis of different geographical regions of biotype C were observed two large groups that show two main entrances of the pathogen in the state of Bahia. Searches done in the database of the Genome Project of C. heterostrophus (JGI- Genome) showed the presence of DNA sequences with similarity to reverse transcriptase of Class I elements belonging to the group Gypsy/Ty3. Based on these sequences could be found seven different copies of an intact transposable element named Sophie. The analysis of 37 sequences of the reverse transcriptase gene showed a possible silencing mechanism similar to RIP. The seven copies of the element Sophie had 7426 bp 7512 bp. The retrotransposon sequences Sophie has two open reading frames (ORFs) that encode the Gag protein and the Pol polyprotein. The presence of different target sites suggests that Sophie is an element with recent activity in the genome of C. heterostrophus can have a great impact on the evolution of the genome of its host. / Retrotransposons do grupo Gypsy/Ty3 são os principais elementos transponíveis encontrados no genoma de fungos fitopatogênicos. Neste trabalho, dois retrotransposons denominados de MpSaci e Sophie foram analisados em Moniliophthora perniciosa e Cochliobolus heterostrophus, respectivamente. MpSaci foi utilizado para avaliar os marcadores moleculares baseados em elementos transponíveis IRAP e REMAP. Quando 70 isolados de M. perniciosa foram analisados, o total de 43 locos foram amplificados gerando 46,51% de bandas polimórficas. Diferenças significativas foram encontradas entre as populações de M. perniciosas divididas em relação ao biótipo e à origem geográfica, demonstrando que as populações encontram-se estruturadas quanto à origem geográfica e ao hospedeiro (biótipo). Pela análise de agrupamento de diferentes regiões geográficas do biótipo C foram observados dois grandes grupos que evidenciam duas principais entradas do patógeno no estado da Bahia. Buscas feitas no banco de dados do Projeto Genoma de C. heterostrophus (JGI - Genome) revelaram a presença de seqüências de DNA com similaridade a transcriptase reversa de elementos da Classe I pertencentes ao grupo Gypsy/Ty3. Com base nessas seqüências foi possível encontrar sete cópias diferentes e intactas de um elemento transponível que foi denominado Sophie. A análise de 37 seqüências do gene da transcriptase reversa demonstrou possível mecanismo de silenciamento semelhante a RIP. As sete cópias do elemento Sophie apresentaram 7.426 pb a 7.512 pb. O retrotransposon Sophie possui duas seqüências de leitura abertas (ORFs) que codificam a proteína Gag e a poliproteína Pol. A presença de diferentes sítios-alvo sugere que Sophie é um elemento com atividade recente no genoma de C. heterostrophus podendo ter grande impacto na evolução do genoma do seu hospedeiro.