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

Les Eléments Transposables (ET) sont des parasites du génome caractérisés par leur capacité à se répliquer plus rapidement que les autres éléments génétiques du génome. La régulation par la voie des piARN joue un rôle essentiel pour limiter l’expansion des ET dans les lignées germinales des animaux.La première question posée est comment le génome répond face à une nouvelle invasion par un ET. Dans ce but, nous avons introduit le transposon de Classe II mariner (sous-famille mos1) chez D. melanogaster, qui ne contient naturellement pas l’élément. Nous avons montré, qu’après son amplification autonome dans le génome, l’élément avait atteint un équilibre en termes de nombre de copies, depuis qu’une régulation de novo par les piARN avait été acquise.Deuxièmement, nous avons étudié la mobilisation de l’élément mariner au cours du processus de colonisation des régions géographiques tempérées. A partir d’un large panel de populations naturelles nous avons trouvé que l’activité moyenne de mariner était remarquablement augmentée dans les populations non-Africaines en comparaison aux populations Africaines. Ces variations peuvent s’expliquer par un fort polymorphisme d’expression (transcriptionnel et traductionnel) des gènes de la voie des piARN.Le troisième chapitre soutient que la forte activité des ET dans la lignée germinale mâle est un phénomène global chez les drosophiles. Par ailleurs, le contenu en ET chez les espèces sœurs (D. melanogaster et D. simulans) a fortement divergé et, cela a affecté la réponse associée à la production des piARN. Chez D. melanogaster, de nombreux « burst » de transposition ont eut lieu récemment. Ces familles d’ET sont activement réprimées par les piARN dans l’ovaire et donc, se retrouvent massivement surexprimés dans les testicules. Chez D. simulans, nous pensons que la réponse par les piARN résulte principalement d’une régulation passée qui semble être la relique d’anciennes invasions d’ET.La voie des piARN est supposé être « garante de l’intégrité du génome » de par son rôle actif dans la défense contre les ET. Cependant, si la sélection naturelle purge les génomes de ces parasites délétères, il semble que les mécanismes de régulation de l’hôte contribuent au maintien de l’homéostasie du génome en limitant leur expansion, et quelque part en favoriser le maintien sur long terme. Ainsi, une autre interprétation pourrait être que la voie des piARN est « garante de la diversification du génome » de par son rôle à faciliter l’accumulation des ET. / Transposable Elements (TEs) are genomic parasites characterized by their ability to replicate faster than any other genetic element in the genomes. The piRNA mediated silencing is of central importance to limit TE expansion in the germline of animal species. The present dissertation explores the relationship between TEs and piRNAs alongside their evolutionary dynamics.The first question raised here was to understand how the genome responds to a new TE invasion. For that purpose, we injected a mariner Class II transposon into D. melanogaster genome that does not naturally contain the element. We found that, after its self-replication into the genome, the element have reached a copy number equilibrium since a de novo piRNA mediated regulation have been acquired.Second, we studied the mariner rewiring activity during the colonization of geographical temperate regions. From a large sampling of D. simulans natural populations, we found the mean activity of mariner to be strikingly higher in non-African populations compared to the African ones. These findings support the idea that selection acting on piRNA effector proteins has been of central importance to explain TE lineages diversification during colonization process.The third chapter provides evidences to propose that, the strong TE activity in testes, is a general phenomenon in Drosophila. We also observed that TE landscape divergence between the two sister species, have affected the genomic response mediated by the piRNAs. As a response of their recent bursts of transposition, TEs overexpressed in testes are preferentially silenced by piRNAs in D. melanogaster ovaries. By contrast, we assumed the D. simulans piRNA response to be the relic of a past regulation that still persists mostly against inactive TEs.The piRNA silencing in the germline, is assumed to be the “vanguard of genome” defense and integrity due to its active role against TEs. However, while natural selection purifies the genome from its deleterious parasites, it seems that the host regulation contributes to genome homeostasis by limiting their expansion, and somehow, favors their longterm maintenance. Thus, another interpretation would have been that piRNA silencing is the “vanguard of genome” diversification due to its active role in facilitating TE accumulation