Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The mesophragmatica group belongs to the radiation virilis-repleta of the Drosophila subgenus, it was established by Brncic and Koref in 1957. The species of this group present some characteristics of isolated endemic species in some places in Andes. The common ancestral of the species of the group seems to have acquired, for selective pressure, genetics structures better adjusted to each region. Although there is just a few studies involving these species and still have to be done in relation to the presence and evolution of transposable elements in its genomes. In this context, the transposable elements of the families, hobo, Tom/17.6, I, mariner, P, micropia and gypsy had been analyzed in species of Drosophila of the mesophragmatica group using, Dot Blot and PCR. The genomic DNA of species D.viracochi, and one of the D. gasici had presented hybridization for the micropia element when analyzed by Dot Blot. Analysis the presence of the TEs of the families Tom, 17.6, hobo was made by PCR. However, they had not been gotten amplicons for none of these elements. However homologous sequences to element P are found in D. gasici and D. pavani. Using probe of the elements I and mariner they had been carried through Dot Blot not presenting hybridization with genomic DNA of species D. pavani, D. brncici, D. viracochi, D. gasici (three different populations). Genomic DNA of species D. pavani, D. brncici, D. viracochi, D. gasici (three different populations) hybridized with probe of the element gypsy also having amplification for PCR for all the analyzed species. The purify products of PCR had been sequenced. Phylogenetic analysis s confirmed the idea that it has incongruence between the phylogeny of the species and of its TEs due to a standard of complex evolution that involves mechanisms as: random losses, vertical and horizontal transference, ancestral polymorphism, different taxes of evolution. Those mechanisms might be not mutually excludable and probably occur simultaneously. / O grupo mesophragmatica pertence à radiação virilis-repleta do sub-gênero Drosophila, foi estabelecido por Brncic & Koref em 1957. As espécies deste grupo apresentam algumas características de espécies endêmicas isoladas em vários locais nos Andes. O ancestral comum das espécies do grupo parece ter adquirido, por pressão seletiva, estruturas gênicas melhor ajustadas a cada região. Embora existam alguns estudos envolvendo estas espécies pouco se sabe em relação à presença e evolução de elementos transponíveis em seus genomas. Neste contexto, os elementos transponíveis das famílias, hobo, Tom/17.6, I, mariner, P, micropia e gypsy foram analisados em espécies de Drosophila do grupo mesophragmatica usando, Dot Blot e PCR. O DNA genômico das espécies D.viracochi, e uma das linhagens de D. gasici apresentaram hibridização para o elemento micropia quando analisadas por Dot Blot. Análise da presença dos TEs das famílias Tom, 17.6, hobo foi feita por PCR. Porém, não foram obtidos amplicons para nenhum destes elementos. No entanto seqüências homólogas ao elemento P estão presentes em D. gasici e D. pavani. Utilizando sonda dos elementos I e mariner foram realizados Dot Blots não apresentando hibridização com DNA genômico das espécies D. pavani, D. brncici, D. viracochi, D. gasici (três linhagens diferentes). DNA genômico das espécies D. pavani, D. brncici, D. viracochi, D. gasici (três linhagens diferentes) hibridizaram com sonda do elemento gypsy havendo também amplificação por PCR para todos as espécies analisadas. Os produtos de PCR purificados foram seqüenciados. Análise filogenética a partir destas seqüências reforçou a idéia de que haja incongruências entre a filogenia das espécies e de seus TEs devido a um padrão de evolução complexa que envolva mecanismos como: perdas estocásticas, transferência vertical e horizontal, polimorfismo ancestral, diferentes taxas de evolução sendo não mutuamente excludentes e provavelmente ocorram simultaneamente.

Orientador: Claudia Marcia Aparecida Carareto / Banca: Marie-Anne Van Sluys / Banca: Elgion Lucio da Silva Loreto / Banca: Ivan de Godoy Maia / Banca: Maria Elisabete Jorge Amaral / Resumo: Elementos de transposição (TEs) são entidades genéticas que podem ter profundos impactos, estrutural, funcional, intra e interespecíficos na evolução dos genomas. A contribuição dos TEs para formação de novas seqüências codificadoras de proteínas é de particular interesse porque sua inserção em exons pode alterar a seqüência protéica influenciando diretamente o fenótipo. Além disso, o estudo das condições que provocam a ativação de TEs, e os mecanismos que os regulam, justifica o interesse de se identificar TEs expressos em tecidos ou condições específicas. Este estudo foca tais questões usando um modelo vegetal: C. arabica, única espécie híbrida e poliplóide do seu gênero, derivada de uma hibridização recente e natural entre C. canephora e C. eugenioides. As análises foram realizadas por meio de uma variedade de abordagens: 1) análises computacionais usando uma combinação de RepeatMasker, tBLASTx e diversas bibliotecas de TEs referência estocadas no Repbase; 2) análises de expressão baseadas em macroarranjos de DNA; e 3) avaliação do número de cópias e distribuição cromossomal de TEs ativos por Hibridização in situ fluorescente (FISH). Foram identificados 180 unigenes com fragmentos de TEs nas três espécies de café. Em uma primeira análise, com base em unigenes selecionados, foi possível sugerir 26 putativas proteínas com inserção de cassetes de TEs, demonstrando uma provável contribuição para a variabilidade do repertório protéico hospedeiro. Por outro lado, 327 ESTs similares a TEs expressos foram identificadas com uma possível abundância diferencial para duas famílias de Ty3/Gypsy (dea1 e Retrosat) identificadas em apenas duas bibliotecas de C. canephora (sementes e pericarpo). Análises de expressão mostraram que muitos dos mRNAs quiméricos e TEs ativos apresentam baixa expressão... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Transposable elements (TEs) are genetic entities that can have profound structural, intra, interspecific impacts in evolution of the genomes. The contribution of the TEs in the protein coding region is of particular interest because insertions of TE into exons can alter the protein sequence influencing directly the phenotype. Moreover, the analysis of the conditions that cause the TE activation and the mechanisms that regulate them justify the interest of identifying expressed TEs in tissues or specific conditions. This study focus such subjects using the plant model: C. arabica, unique hybrid species and polyploidy of their genus, derived of a recent and natural hybridization between C. canephora and C. eugenioides. The analyses were performed by a variety of approaches: 1) computational analyses using a combination of RepeatMasker, tBLASTx e several libraries of reference TEs stored in Repbase; 2) expression analysis based in macroarrays; and 3) evaluation of copy number e chromosomal distribution of expressed TEs by Fluorescent in situ hybridization (FISH). 180 unigenes containing TE fragments were identified in the three Coffea species. Based in selected unigenes, it was possible to identify 26 putative proteins harboring TE-cassettes, demonstrating a probable contribution for the host protein repertory variability. In addition, 327 ESTs similar to expressed TEs were identified with a probable differential abundance for two families of Ty3/Gypsy (dea1 and Retrosat) identified only in two cDNA libraries from C. canephora (seeds and pericarp). Our expression analyses showed that most of the chimerical mRNAs and expressed TEs has low or null expression. On the other hand, several transcripts had their expression reestablished in cell culture treated with Cycloheximide, a drug that permit the accumulation of transcripts previously silenced by reverting a mechanisms... (Complete abstract click electronic access below) / Doutor

Les génomes des espèces aviaires ont des caractéristiques particulières comme la structure des chromosomes et le contenu en séquences répétées. En effet, alors que dans les génomes vertébrés, la proportion de répétitions dans le génome varie de 30 à 55 %, dans les espèces aviaires, cette proportion est plus faible et varie de 8 à 10 %. L’annotation du contenu répété est le plus souvent réalisée avec le programme RepeatMasker qui s’appuie généralement sur la banque de séquences répétées Repbase. Ce genre de méthode repose uniquement sur la séquence des éléments transposables connus. De fait, ce programme n’est pas en mesure de détecter de nouvelles séquences répétées, et la qualité de l’annotation sera donc dépendante de la banque de séquences d’éléments transposables utilisée. De plus en plus d’études montrent que les éléments transposables jouent un rôle dans le fonctionnement du génome et peuvent influer sur l’expression des gènes. Il est donc primordial que l’annotation de ces séquences soit la plus complète possible. Au cours de ma thèse a été mise en place une stratégie d’annotation des séquences répétées que nous avons élaborée et appliquée à un génome de grande taille, celui de la poule rouge de jungle. L’annotation ainsi obtenue m’a permis d’étudier l’organisation du génome de cette espèce au travers de ses séquences répétées et éléments transposables. / The genomes of avian species have special features such as the structure of chromosomes or their content in repeated sequences. Indeed, compared to vertebrate genomes in which the amount of repetitions varies from 30 to 55%, it is lower in avian species and varies from 8 to 10%. The annotation of repeated content is most often done with the RepeatMasker program that is generally use the Repbase database of repeated sequences. This kind of approach is based solely on the sequence of already known transposable elements. In fact, this program is not able to detect new repeats and in consequence produced annotations with a quality that depends on the sequences of transposable elements used. More and more studies show that transposable elements play a role in the functioning of the genome and can influence gene expression. It is therefore essential that the annotation of these sequences is as complete as possible. There are many programs using methods for detecting de novo transposable elements, either by searching for characteristic structures, or by comparing the genome against itself. However, no standard strategy of annotation for repeated sequences have been defined yet. My thesis aims to set-up a standard strategy of annotation for repeated sequences that was applied to a large genome, that of the red jungle fowl. The obtained annotation allowed me studying the genome organization in this species through its repeated sequences and transposable elements.

DNA methylation entails the addition of a methyl group to the 5-carbon of the cytosine base of the DNA. This modification is important during many biological processes such as imprinting, X-chromosome inactivation, cell differentiation as well as silencing of transposable elements (TEs). DNA methylation is dynamic during early mammalian development, despite being a more static mark in somatic cells. Global hypomethylation is a hallmark of epigenetic reprogramming in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). Genome integrity is crucial during early development, as the germline DNA needs to be protected for future generations. Therefore, epigenetic reprogramming presents a critical phase for TE defence since presumably alternative silencing pathways need to be employed to limit their activity. In this thesis, I investigate the role of small RNAs to control TEs during global waves of DNA demethylation in cellular reprogramming, naïve pluripotency as well as early mammalian development. Following an introduction to the research questions, in chapter 3 I investigate the mechanism of TE regulation in an in vitro model of Dnmt1 deletion in mouse ES cells to recapitulate in vivo epigenetic reprogramming. I find that certain classes of TEs become transcriptionally upregulated and subsequently resilenced by a mechanism independent of DNA methylation. I identify ARGONAUTE 2 (AGO2) bound siRNAs as the prominent mechanism to control certain classes of TEs, while others appear to be regulated by redistribution of repressive histone modifications. In chapter 4, I construct Dicer constitutive and conditional KO ESCs in the background of the Dnmt1f l/f l ESCs using CRISPR-Cas9. I dissect the role of DNA methylation and of DICER dependent small RNAs on transcriptional changes of ESCs. Additionally, I find that DICER dependent small interfering RNAs (siRNAs) re-silence transcriptionally active TE classes. Finally, in chapter 5, I examine the role of small RNAs in TE silencing in different models of global hypomethylation in vivo and in vitro PGCs, during iPSC reprogramming and in a transition from serum to 2i culturing of mouse ESCs.

Made available in DSpace on 2014-08-20T13:32:46Z (GMT). No. of bitstreams: 1 dissertacao_gabriela_dos_santos.pdf: 1447365 bytes, checksum: 9a964998717dab34fd1a25c9caf8d86c (MD5) Previous issue date: 2013-03-05 / The breeding programs have made significant contributions to obtain more productive genotypes. Studies in Plant biotechnology has been one of the tools to aid plant breeding, as well as the use of molecular markers. Transposons and Retrotransposons are ubiquitous in plant genomes and are increasingly studied. This study aimed to evaluate the genetic similarity among different rice cultivars using the techniques of IRAP and REMAP using the presence of retrotransposons. To verify this similarity was performed in 20 rice genotypes (Brazilian, Japanese and Filipinos) a DNA extraction for subsequent PCR amplification using the techniques IRAP and REMAP. Analysis of amplification products was made by classifying the fragments as independently presence and absence of amplification at different heights polyacrylamide gel for data were used to construct a binary matrix. The data generated were used for the calculation of genetic similarity between all pairs of individuals with the aid of the computer program NTSYS pc 2.1. To describe the patterns of similarity was adopted Dice coefficient and a dendrogram was constructed by the method of unweighted UPGMA grouping in pairs. Furthermore, was estimated cophenetic correlation coefficient (r), according to the Mantel test and statistical stability of the grouping was estimated by analysis of bootstrapping with 1000 replicates through the computer program WinBoot 1.0. The results of this work show that it is possible to assess the genetic variability in rice genotypes using IRAP and REMAP techniques through the use of retrotransposons as molecular markers. / Os programas de melhoramento genético têm contribuído para a obtenção de genótipos mais produtivos. Estudos em Biotecnologia vegetal tem sido uma das ferramentas de auxílio para o melhoramento genético vegetal, assim como a utilização dos marcadores moleculares. Transposons e Retrotransposons são onipresentes no genoma das plantas e são cada vez mais estudados. Esse trabalho teve como objetivo avaliar a similaridade genética entre diferentes cultivares de arroz utilizando as técnicas de IRAP e REMAP utilizando a presença de retrotransposons. Para verificar essa similaridade, foi realizada em 20 genótipos de arroz (brasileiros, japoneses e filipinos) a extração de DNA, para posterior amplificação por PCR utilizando as técnicas IRAP e REMAP. A análise dos produtos da amplificação foi feita classificando os fragmentos independentemente conforme presença e ausência de cada fragmento amplificado em diferentes alturas do gel de poliacrilamida para que os dados fossem utilizados na construção de uma matriz binária. Os dados gerados foram utilizados para o cálculo de similaridade genética entre todos os pares de indivíduos, com o auxílio do programa computacional NTSYS pc 2.1. Para descrever os padrões de similaridade foi adotado o coeficiente de Dice e foi construído um dendrograma por meio do método não-ponderado de agrupamento aos pares UPGMA. Além disso, foi estimado o coeficiente de correlação cofenética (r), de acordo com o teste de Mantel e a estabilidade estatística do agrupamento foi estimada por meio da análise de bootstraping com 1000 replicações, através do programa computacional WINBOOT. Os resultados obtidos neste trabalho mostram que é possível avaliar a variabilidade genética em genótipos de arroz utilizando as técnicas IRAP e REMAP através do uso dos retrotransposons como marcadores moleculares.

Les éléments transposable (ET) sont des séquences d'ADN qui ont la capacité de se déplacer au sein des génomes. Pour contrebalancer les effets négatifs liés à l'activité des ET, il existe chez leurs hôtes des mécanismes régulant l'activité de transposition. Une fois qu'un ET est régulé, l'accumulation progressive de mutations dans sa séquence conduit fatalement à la perte définitive de son activité de transposition. J'ai cherché au cours de cette thèse à mieux comprendre le succès et le maintien de ces séquences répétées, avec d'une part l'étude des transferts horizontaux (TH) d'ET, un moyen d'échapper aux mécanismes de régulation , et d'autre part l'étude de leur régulation. Dans la première partie de ma thèse, je me suis intéressé à l'étude des TH entre deux espèces proches de drosophiles. Dans cette étude, j'ai développé une nouvelle méthode bioinformatique permettant la détection de séquences transférées horizontalement entre deux génomes eucaryotes qui m'a permis détecter de nombreux TH d'ET. Ce travail m'a aussi conduit à développé une nouvelle méthode de contrôle du taux de faux positifs moyen applicable aux tests multiples unilatéraux. Dans la deuxième partie de ma thèse, j'ai étudié la régulation des ET par la voie des petits ARN, un mécanisme de l'ARN interférence. Dans cette étude, j'ai analysé des données de séquençage de petits ARN, ainsi que d'ARN totaux issues de différentes populations de D. simulans. Ce travail a conduit au développement d'un pipeline d'analyse permettant d'étudier des différences d'expression entre des séquences répétées ainsi que d'une nouvelle procédure de contrôle qualité de ce type de donnée / Transposable elements (TEs) are repeated DNA sequences that are able to move (transpose) within their host genome. To counteract the negative effects of their TEs, regulation mechanisms of the TE transposition are present in the host genome. Once a TE is regulated, the progressive accumulation of mutations in its sequence will inevitably lead to the definitive loss of its transposition capacity. My work during this thesis is was to better understand the succss and the maintaining of these peculiar repeated sequencest, with the study of horizontal transfers (HTs) of TEs enabling them to escape host regulation mechanisms, and the study of this regulation. The first part of my thesis concerns the study of HTs between two closely related drosophila species. I have developed a new bioinformatic method for the detection of HTs between two eukaryotic genomes. The development of this method brought me to work on the unilateral multiple testing problematic for which I have developed a new procedure to control the expected false discovery rate (FDR). The second part of my thesis focuses on the regulation of TEs by the small RNA pathway, an RNA interference mechanism. For this study, I have analyzed sequencing data of small RNAs and total RNAs. For this work, I have developed an analysis pipeline, to study differences of expression between repeated sequences. Some features of the small RNA dataset required the development of a new procedure to parse them. This procedure was extended and implemented in a software to be used for the quality control of next generation sequencing data

Les éléments transposables (ET) sont des constituants majeurs des génomes eucaryotes. Leur mobilisation joue un rôle important dans l'évolution et l'adaptation des organismes. Cependant, la transposition des ET peut conduire à des dommages irréversibles du génome et elle doit donc être étroitement contrôlé. Chez Drosophila melanogaster, la transposition des ET est contrôlée par les siRNA (small interfering RNAs) et les piRNA (Piwi-interacting RNAs) qui agissent en réprimant des cibles ARN de séquences complémentaires. Les siRNA et piRNA ont des modes distincts de biogenèse, de reconnaissance de cibles et d'activité repressive. Les piRNAs sont seulement présents en abondance dans les gonades, et transmis maternellement aux embryons. Par une approche de séquençage à haut débit, j'ai pu montrer que bien qu'ils induisent une répression transcriptionnelle des ET à ce stade du développement, ils sont pratiquement absents des têtes de drosophiles adultes. Cet état est cependant hérité et il est suffisant pour limiter l'expression des ET dans l'adulte, même en l'absence de siRNA. A l'inverse, si la répression transcriptionnelle précoce n'est pas établie, les siRNA agissent comme un système de sauvegarde en limitant l'expression des ET. En cas de perte conjointe des piRNA et siRNA, l'expression des ET augmente significativement et la durée de vie des mouches adultes se trouve réduite. Les analyses de sequences à grande échelle m'ont par ailleurs conduit à développer des outils logiciels intégrés dans Galaxy et à m'impliquer significativement dans la communauté qui développe ce système au niveau international. / Transposable elements are major components of eukaryotic genomes and have been proposed as important drivers of gene network evolution, as they can move or “transpose” in their host genome, creating gene duplications, gene inactivations or altogether altering gene function. Nevertheless, uncontrolled high-rate transposition leads to DNA damage and genomic instabilities, and therefore needs to be kept at a low level. In the fruitfly Drosophila melanogaster, transposition is counteracted by multiple mechanisms, amongst which the generation of small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). siRNAs and piRNAs belong to the category of small RNAs, and these are involved in negative regulation of complementary target RNAs abundance, but siRNAs and piRNAs have distinct mechanisms of biogenesis, target recognition and mechanisms of target regulation. Notably, piRNAs are only abundant in gonads and are transmitted to the embryo. By sequencing small RNAs and normal transcripts in adult heads, I conclude that, while piRNAs are likely absent in adult heads, they induce a repressive state on TEs. If this repressive state is lost, the siRNA pathway can compensate and limit Transposable element levels. If siRNAs are lost, the repressive state induced by piRNAs suffices to limit Transposable element levels. If both piRNAs and siRNAs are lost, the expression level of Transposable elements increases, and flies have a shorter life span. The requirement to analyse large-scale sequencing data led to the development of multiple tools for the reproducible research platform Galaxy.

Le moustigre tigre Aedes albopictus, un des vecteurs de la Dengue et du Chikungunya, est une espèce invasive qui a colonisé le monde entier en 30 ans à partir de son berceau asiatique. Les éventuelles bases génétiques de ce succès sont inconnues. Afin d’étudier l’ampleur de la différenciation génétique entre populations asiatiques et européennes et la part prise par la sélection naturelle dans cette différenciation, nous avons développé de nouveaux marqueurs génétiques reposant sur le polymorphisme d’insertion des éléments transposables. Pour cela, nous avons dans un premier temps conçu un outil bioinformatique –dnaPipeTE— nous permettant de dresser le portrait de la fraction répétée du génome d’Ae. albopictus à partir d’une faible proportion des lectures brutes issues d’un projet de séquençage en cours. Le polymorphisme d’insertion de cinq des familles d’ET décrites a ensuite été étudié par la technique de transposon display couplée à du séquençage Illumina, chez 140 individus issus de trois populations vietnamiennes et cinq populations européennes. L’immense majorité des 128 000 marqueurs analysés montre une différenciation génétique très faible entre Europe et Asie. Nous avons néanmoins pu mettre en évidence un centaine d’insertions ayant des fréquences extrêmement différentes entre ces continents. La majorité d’entre elles ségrège à forte fréquence en Europe, suggérant une adaptation du moustique à son environnement tempéré / The Asian tiger mosquito, one of the main vectors of Dengue and Chikungunya, is an invasive species that colonized the world during the last 30 years from its cradle in Asia. Whether this success has an underlying genetic basis remains to be investigated. In order to study the extent of the genetic differentiation between Asian and European populations and the contribution of natural selection to this differentiation, we developed new genetic markers based on transposable elements insertion polymorphism. We first conceived a bioinformatic pipeline –dnaPipeTE— that allowed to grasp a comprehensive picture of the repetitive fraction of the Tiger’s genome through the analysis of a low proportion of raw reads from a ongoing sequencing project. The insertion polymorphism of five transposable element families was then studied by Illumina based transposon display, in 140 individuals from three Vietnamese populations and five European populations. The vast majority of the 128,000 markers showed a very low genetic differentiation between Europe and Asia. However 92 of them displayed extreme frequency differences between the continents. The majority of them segregate at high frequencies in Europe, a pattern suggestive of adaptive evolution towards temperate environments

Les éléments transposables sont des composants majeurs de la plupart des génomes, et leur impact sur l’évolution des génomes est maintenant bien documenté. Cependant, la manière par laquelle ils participent au transcriptome n’est pas encore clairement établie. En utilisant le génome séquencé de Drosophila melanogaster et les bibliothèques d’EST, nous avons déterminé les insertions d’éléments transposables qui sont transcrites sans équivoque, ainsi que leur localisation dans le génome séquencé de D.melanogaster. Nous montrons que la plupart des familles d’éléments transposables sont transcrites, et nous identifions spécifiquement 69 insertions d’éléments transposables exprimés, dont la moitié réside dans des gènes, la plupart dans des introns et des régions régulatrices 5’UTR. / Transposable elements (TEs) are major components of most genomes, and their impact on genome evolution is now well documented. However, the way they affect the transcriptome is still not clearly established. Using the sequenced genome of Drosophila melanogaster and EST libraries (“Expressed Sequence Tag”, large tags (~500bp) corresponding to subsequences of a transcribed cDNA sequences), we describe here the TE insertions that are unequivocally transcribed, and we have determined their location in the sequenced genome of Drosophila melanogaster. We show that most TE families are transcribed, and we have specifically identified 69 expressed TE insertions, half of which are located inside genes, mostly within introns and 5′UTRs regulatory regions.

Os elementos de transposição (TEs) se movimentam de um locus para outro no genoma afetando a estrutura e evolução destes. A superfamília de transposases hAT é definida pelos elementos que compartilham os domínios de dimerização e ligação ao DNA com os transposons previamente descritos: hobo, Activator e Tam3. Análises prévias encontraram algumas evidencias da presença genômica e ativação transcricional de TEs relacionados à superfamília hAT em cana-de-açúcar (denominados de família SChAT) e pelo menos três linhagens evolutivas foram postuladas. O objetivo deste trabalho é caracterizar versões genômicas das linhagens de transposons (191 e 257) e linhagem possivelmente domesticada (074). Pretende-se estudar as relações evolutivas, distribuição em gramíneas, identificar os padrões de expressão e propriedades funcionais. Regiões de sintenia foram estabelecidas para estes BACs em Arabidopsis thaliana, Brachypodium distachyon, Sorghum bicolor, Oryza sativa e Zea mays. Elementos relacionados com as três linhagens foram procurados nestes genomas. / Transposable elements (TEs) are able to move from one locus to another within a genome. TE mobilization affects genome structure and evolution. The hAT transposase superfamily is defined as elements that share the dimerization and DNA ligation domains with the previously described hobo, Activator and Tam3 transposon elements. Previous analyses found some genomic and transcriptional evidences of TEs related to hAT superfamily in sugarcane (named SChAT family) and at least three evolutionary lineages were proposed. The aim of this work is to characterize full-length genomic versions of the transposons lineages (191 and 257) and from the domesticated lineage (074). It is proposed to study the evolutionary relationship, distribution along grasses genomes, identify expression patterns and functional capacities of the SChAT elements. Syntenic regions for the BACs containing elements from the three lineages were mapped in Arabidopsis thaliana, Brachypodium distachyon, Sorghum bicolor, Oryza sativa and Zea mays. Related elements were search on the same genomes.