MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression via inhibiting mRNA translation or degrading mRNA. Since the discovery of miRNAs, dysregulated miRNAs have been identified in human patients with various diseases. Moreover, the role of miRNAs in biological processes, including immune homeostasis and autoimmunity pathogenesis, has been widely investigated. Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease that causes systemic damage to multiple organs and is characterized by the production of pathogenic autoimmune antibodies. In previous work in my lab, a set of commonly upregulated miRNAs in splenic lymphocytes of three lupus-prone mouse models was identified, including the miR-183-96-182 cluster (miR-183C) and miRNAs located at DLK1-DIO3 region. The work presented in this dissertation focuses on comparing the dysregulation pattern of miRNAs from different cell sources of lupus-prone mice and investigating the potential role of miR-183C in the pathogenesis of SLE and inflammation. The first goal was to test whether dysregulated miRNAs initially identified in the spleen of MRL/lpr mice, a standard model for SLE, is also reflected in the peripheral blood mononuclear cells (PBMCs) as PBMC is the primary source of lymphocytes in human patients. In MRL/lpr mice, we found that dysregulated miRNAs in PBMCs were overall comparable to those identified in the splenic lymphocytes. Further, comparing dysregulated miRNAs between mice and humans showed a similarity in the dysregulation of miRNAs in PBMCs of murine and human lupus. Among the upregulated miRNAs, the expression of three miRNAs of miR-183C was found to be commonly upregulated. To investigate the role of miR-183C, we developed miR-183C in CD2+ cells of C57BL/6 Faslpr/lpr (miR-183C-/-B6/lpr) mice. In miR-183C-/-B6/lpr mice, we observed a significantly reduced level of anti-dsDNA in the serum and IgG immunocomplex deposition in the kidney. Importantly, in vitro inhibition of miR-183C in activated splenic lymphocytes led to reduced production of the proinflammatory cytokine, IFN, and Foxo1, a transcription factor that is a target of miR-183C miRNAs. I also tested for miRNA changes in C57BL/6 Faslpr/lpr mice with conditional deletion of Early Growth Response-2 (EGR2) (Egr2-/- B6/lpr), another knockout mouse developed in our laboratory. Egr2 has recently been shown to regulate immunity and autoimmunity and play a role in lupus. An unexpected observation is that Egr2-/-B6/lpr mice had significantly reduced expression of a group of lupus-related miRNAs that are located at the genomic imprinted DLK1-DIO3 locus. Given that the upregulation of DLK1-DIO3 miRNAs in lupus is subjected to DNA methylation regulation and that the epigenetic regulatory role of EGR2 is emerging in recent studies, reduced representative bisulfite sequencing (RRBS) was performed to evaluate the methylation changes induced by Egr2 deletion. Global DNA hypomethylation and methylation changes at specific sites at DLK1-DIO3 region were noticed in CD4+ T cells of Egr2-/-B6/lpr mice. Overall, our research suggested a therapeutic effect of inhibiting the miR-183C expression on SLE. The interplay between epigenetic factors could help expand the possibility of controlling epigenetic regulators in autoimmune disease treatment. / Doctor of Philosophy / Systemic lupus erythematosus (SLE) is an autoimmune disease that causes damage to multiple organs. Same with other autoimmune diseases, the exacerbated immune reaction to self-antigen and auto-reactive adaptive immune cells were described in SLE. Currently, the treatment of lupus mainly uses immunosuppressive drugs to inhibit the global immune reaction. Thus, the innovative drug is desperately needed for SLE patients. MicroRNAs (miRNAs) are small RNAs that inhibit the expression of genes by binding to mRNAs in a complimentary manner. Since the discovery of the first microRNA, the pivotal role of microRNAs in immunity and autoimmunity was vigorously investigated. Our lab was the first to describe a set of miRNAs that are commonly upregulated in three murine lupus models. Among these miRNAs, miR-183, miR-96, and miR-182 belong to the miR-183-96-182 cluster (miR-183C). The aim of the study in this dissertation focused on illuminating the dysregulation pattern of miRNAs in different cell sources in the murine lupus model and the role of miR-183C in the pathogenesis of SLE. We found that miRNAs are similarly dysregulated in peripheral blood mononuclear cells and splenic lymphocytes of MRL/lpr mice. Then we conditionally knocked out the miR-183C in B6/lpr mice and investigated the effect of miR-183C loss on the pathogenesis of autoimmunity. Importantly, we found that the deletion of miR-183C led to a reduced production level of autoantibodies and ameliorated the deposition of immune complexes in the kidney. Moreover, the production of proinflammatory cytokines of splenic lymphocytes was regulated by miR-183C as well. Besides miR-183C, I also investigated the effect of early growth response 2 (EGR2), a transcription factor, on the expression of a set of lupus-related miRNAs and the methylation change at the genome location of these miRNAs. In summary, miR-183C can be a potential therapeutic target for lupus treatment while clinical human studies are needed to better clarify the effectiveness and efficiency.

no / The nucleus is a complex and highly compartmentalized organelle, which undergoes major organization changes during cell differentiation, allowing cells to become specialized and fulfill their functions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes a programmed transformation from active status, associated with execution of the genetic programs of cornification and epidermal barrier formation, to a fully inactive condition and becomes a part of the keratinized cells of the cornified layer. Tremendous progress achieved within the past two decades in understanding the biology of the nucleus and epigenetic mechanisms controlling gene expression allowed defining several levels in the regulation of cell differentiation–associated gene expression programs, including an accessibility of the gene regulatory regions to DNA–protein interactions, covalent DNA and histone modifications, and ATP-dependent chromatin remodeling, as well as higher-order chromatin remodeling and nuclear compartmentalization of the genes and transcription machinery. Here, we integrate our current knowledge of the mechanisms controlling gene expression during terminal keratinocyte differentiation with distinct levels of chromatin organization and remodeling. We also propose directions to further explore the role of epigenetic mechanisms and their interactions with other regulatory systems in the control of keratinocyte differentiation in normal and diseased skin.

During tissues development multipotent progenitor cells establish tissue-specific gene expression programmes, leading to differentiation into specialized cell types. It has been previously shown that the transcription factor p63, a master regulator of skin development, controls the expression of adhesion molecules and essential cytoskeleton components. It has also been shown that p63 plays an important role in establishing distinct three-dimensional conformations in the Epidermal Differentiation Complex (EDC) locus (Fessing et al., 2011). Here we show that in p63-null mice about 32% of keratinocytes showed altered nuclear morphology. Alterations in the nuclear shape were accompanied by decreased expression of nuclear lamins (Lamin A/C and Lamin B1), proteins of the LINC complex (Sun-1, nesprin-2/3) and Plectin. Plectin links components of the nuclear envelope (nesprin-3) with cytoskeleton and ChIP-qPCR assay with adult epidermal keratinocytes showed p63 binding to the consensus binding sequences on Plectin 1c, Sun-1 and Nesprin-3 promoters. As a possible consequence of the altered expression of nuclear lamins and nuclear envelope-associated proteins, changes in heterochromatin distribution as well as decrease of the expression of several polycomb proteins (Ezh2, Ring1B, Cbx4) has been observed in p63-null keratinocytes. Moreover, recent data in our lab have showed that p63 directly regulates Cbx4, a component of the polycomb PRC1 complex. Here we show that mice lacking Cbx4 displayed a skin phenotype, which partially resembles the one observed in p63-null mice with reduced epidermal thickness and keratinocyte proliferation. All together these data demonstrate that p63-regulated gene expression program in epidermal keratinocytes includes not only genes encoding adhesion molecules, cytoskeleton proteins (cytokeratins) and chromatin remodelling factors (Satb1, Brg1), but also polycomb proteins and components of the nuclear envelope, suggesting the existence of a functional link between cytoskeleton, nuclear architecture and three dimensional nuclear organization. Other proteins important for proper epidermal development and stratification, are cytokeratins. Here, we show that keratin genes play an essential role in spatial organization of other lineage-specific genes in keratinocytes during epidermal development. In fact, ablation of keratin type II locus from chromosome 15 in epidermal keratinocytes led to changes in the genomic organization with increased distance between the Loricrin gene located on chromosome 3 as well as between Satb1 gene located on chromosome 17 and keratin type II locus, resulting in a more peripheral localization of these genes in the nucleus. As a possible consequence of their peripheral localization, reduced expression of Loricrin and Satb1 has also been observed in keratins type II-deficient mice. These findings together with recent circularized chromosome conformation capture (4C) data, strongly suggest that keratin 5, Loricrin and Satb1 are part of the same interactome, which is required for the proper expression of these genes and proper epidermal development and epidermal barrier formation. Taken together these data suggest that higher order chromatin remodelling and spatial organization of genes in the nucleus are important for the establishment of lineage-specific differentiation programs in epidermal progenitor cells. These data provide an important background for further analyses of nuclear architecture in the alterations of epidermal differentiation, seen in pathological conditions, such as psoriasis and epithelial skin cancers.

No description available.

The overall goal of my work was to develop and apply new chemical methods for the study of epigenetic DNA and protein modifications. In Chapter 3 the development of Suzuki-Miyaura cross coupling (SMcc) for the post-synthetic modification of DNA is described. DNA modification by SMcc is efficient (4-6h) and proceeds under mild conditions (37°C, pH 8.5). The incorporation of various groups useful for biological investigations is demonstrated using this methodology. Using a photocrosslinker, introduced into the DNA by SMcc capture experiments are performed to identify potential binding partners of modified DNA. In Chapter 4 a dehydroalanine (Dha) based chemical protein modification method is described that enables the introduction of posttranslational modification (PTM) mimics into histones. The PTM mimics introduced by this method are tested using western- and dot-blot and binding and enzymatic assays, confirming they function as mimics of the natural modifications. Chapter 5 describes the use of a generated PTM mimics to elucidate the function of O-linked β-Nacetylglucosamine (GlcNAc) of histones in transcriptional regulation. It is shown that GlcNAcylation of Thr-101 on histone H2A can destabilize nucleosome by modulating the H2A/B dimer – H3/H4 tetramer interface. N- and C-terminal histone tails play an important role in transcriptional regulation. In Chapter 6, nuclear magnetic resonance is used to investigate the structure of the histone H3 N-terminal tail in a nucleosome. The H3 tail, while intrinsically disordered, gains some α-helical character and adopts a compact conformation in a nucleosome context. This H3 tail structure is shown to be modulated by Ser-10 phosphorylation. The effect of a new covalent DNA modification, 5- hydroxymethylcytosine (5hmC), on transcription factor binding is investigated in Chapter 7. 5hmC influences HIF1α/β, USF and MAX binding to their native recognition sequence, implying involvement of this modification in epigenetic regulation.

La toxoplasmose, déterminée par le parasite Toxoplasma gondii, est l'une des infections les plus répandues au monde, en raison de la persistance à vie sous forme latente de ce parasite au sein de ces hôtes. Ce parasite fait partie des Apicomplexa et détourne les voies de signalisation de l'hôte par des mécanismes épigénétiques qui convergent vers des protéines nucléaires clés. Nous rapportons ici une nouvelle stratégie de persistance parasitaire impliquant la protéine de rhoptries ROP16 de T. gondii, sécrétée précocement lors de l'invasion, qui cible le facteur de transcription UHRF1 (Ubiquitin-like containing PHD and RING fingers domain 1) et induit un arrêt du cycle de la cellule-hôte. Ceci est induit par l'activité de la DNMT et le remodelage de la chromatine au niveau du promoteur du gène de la cycline B1 par le recrutement d’UHRF1 phosphorylé associé à un complexe protéique multienzymatique répressif. Cela conduit à la désacétylation et à la méthylation de l'histone H3 entourant le promoteur de la cycline B1 pour réduire de manière épigénétique son activité transcriptionnelle. De plus, l'infection par T. gondii provoque une hyper-méthylation de l'ADN dans la cellule hôte par la régulation positive des DNMTs. ROP16 est déjà connue pour activer et phosphoryler des facteurs de transcription de l'immunité protectrice tels que STAT 3/6/5 et le suppresseur tumoral p53 impliqué dans la progression du cycle cellulaire. De plus, ROP16 module ces voies de signalisation de l'hôte de manière souche-dépendante. Comme dans le cas de STAT3, les effets de ROP16 sur UHRF1 dépendent du polymorphisme d'un seul acide aminé du domaine kinase de ROP16. Ce travail montre que Toxoplasma module un nouvel initiateur épigénétique, UHRF1, via un événement précoce initié par la kinase parasitaire ROP16. / Toxoplasmosis, caused by the apicomplexan parasite Toxoplasma gondii, is one of the most common infections in the world due to the lifelong persistence of this parasite in a latent stage in its hosts. T. gondii hijacks host signaling pathways through epigenetic mechanisms which converge on key nuclear proteins. Here we report a new parasite persistence strategy involving Toxoplasma rhoptry protein ROP16 secreted early during invasion, which targets the transcription factor UHRF1 (Ubiquitin-like containing PHD and RING fingers domain 1), and leads to host cell cycle arrest. This is mediated by DNMT activity and chromatin remodeling at the cyclin B1 gene promoter through recruitment of phosphorylated UHRF1 associated with a repressive multienzymatic protein complex. This leads to deacetylation and methylation of histone H3 surrounding the cyclin B1 gene promoter to epigenetically silence its transcriptional activity. Moreover, T. gondii infection causes DNA hypermethylation in its host cell, by upregulation of DNMTs. ROP16 is already known to activate and phosphorylate protective immunity transcription factors such as STAT 3/6/5 and the tumor suppressor p53 involved in cell cycle progression. Moreover, ROP16 modulates host signaling pathways in a strain-dependent manner. Like in the case of STAT3, the strain-dependent effects of ROP16 on UHRF1 can be attributed to a single amino-acid polymorphism in ROP16. This study demonstrates that Toxoplasma hijacks a new epigenetic initiator, UHRF1, through an early event initiated by the ROP16 parasite kinase.

Epigenetic regulatory mechanisms play important roles in the control of lineage-specific differentiation during development. However, mechanisms that regulate higher-order chromatin remodelling and transcription of keratinocyte-specific genes that are clustered in the genome into three distinct loci (Keratin type I/II loci and Epidermal Differentiation Complex (EDC)) during differentiation of the epidermis are poorly understood. By using 3D-Fluorescent In Situ Hybridization (FISH), we determined that in the epidermal keratinocytes, the KtyII and EDC loci are located closely to each other in the nuclear compartment enriched by the nuclear speckles. However, in KtyII locus knockout mice, EDC locus moved away from the KtyII locus flanking regions and nuclear speckles towards the nuclear periphery, which is associated with marked changes in gene expression described previously. Chromatin architectural protein Ctcf has previously been implicated in the control of long-range enhancer-promoter contacts and inter-chromosomal interactions. Ctcf is broadly expressed in the skin including epidermal keratinocytes and hair follicles. Conditional Keratin 14-driven Ctcf ablation in mice results in the increase of the epidermal thickness, proliferation, alterations of the epidermal barrier and the development of epidermal pro-inflammatory response. Epidermal barrier defects in Krt14CreER/Ctcf fl/fl mice are associated with marked changes in gene expression in the EDC and KtyII loci, which become topologically segregated in the nucleus upon Ctcf ablation. Therefore, these data suggest that Ctcf serves as critical determinant regulating higher-order chromatin organization in lineage-specific gene loci in epidermal keratinocytes, which is required for the proper control of gene expression, maintenance of the epidermal barrier and its function.

Les longs ARN non codants (lncRNAs) sont définis comme des transcrits de plus de 200nt et n'ayant pas de potentiel codant. Des études récentes ont démontré que les lncRNAs pouvaient être impliqués dans la régulation de la transcription, de la traduction, de la différenciation cellulaire, de l'expression génique, du cycle cellulaire et des modifications de la chromatine. De plus, il a été montré un impact fonctionnel de certains lncRNAs dans le processus de cancérogenèse mais nos connaissances actuelles sur ces molécules dans le cancer, et plus particulièrement dans la leucémie, restent extrêmement limitées. Au cours de cette étude, nous avons analysé l'expression des lncRNAs par RNA-sequencing sur 40 patients atteints de leucémie aiguë myéloblastique (LAM) à caryotype normal. Parmi les 11065 lncRNAs exprimés dans nos échantillons, nous avons identifié une signature de lncRNAs associée à la mutation de NPM1. Afin de mettre en évidence les fonctions putatives des lncRNAs sélectionnés, nous avons utilisé un algorithme de prédiction d'interaction protéine/ARN. De manière intéressante, plus de la moitié des lncRNAs présentent des sites d'interactions potentiels à SUZ12, une sous unité du complexe PRC2 (Polycomb repressive complex 2), connu pour être recruté par des lncRNAs pour la régulation épigénétique de gènes cibles. Par RNA immunoprécipitation (RIP) de SUZ12, nous avons pu démontrer que le lncRNA XLOC_087120 interagissait avec SUZ12. De plus, son expression est anti-corrélée avec celle des gènes voisins codants des histones, suggérant un rôle dans la régulation négative des histones par ce lncRNA. L'impact de la dérégulation de XLOC_087120 sur les histones a été confirmé par des expériences de surexpression et d'inhibition de ce lncRNA dans des lignées de LAM. De plus, même si la mutation NPM1 ne semble pas affecter directement l'expression de ce lncRNA, des expériences d'infection de la forme mutée de NPM1 dans une lignée LAM ont montré que NPM1 pourrait réguler la localisation nucléaire/cytoplasmique de XLOC_087120 et moduler sa fonction de répresseur. En conclusion, ces données suggèrent que les lncRNAs sont des facteurs clés dans la pathogenèse des LAMs. / Long noncoding RNAs (lncRNAs) are defined as RNA transcripts that are larger than 200 nt but do not appear to have protein- coding potential. Recent studies have demonstrated that lncRNAs regulate many processes such as transcription, translation, cellular differentiation, gene expression regulation, cell cycle regulation, and chromatin modification. Cumulative evidence points towards an important role of lncRNAs in cancer initiation, development, and progression. However, our overall knowledge of lncRNAs in cancer, including leukemia, remains extremely limited. In this study, we investigated lncRNA expression by RNA-sequencing in 40 acute myeloid leukemia (AML) patients with normal karyotype. Among 11065 lncRNA expressed in our samples, we identified specific lncRNA signature associated with the presence of NPM1 mutation. To go further into the putative function of these lncRNAs, we used catRAPID Omics algorithm to predict potential protein partners. Interestingly, the majority of the selected lncRNAs contains putative SUZ12 binding sites, a PRC2 (Polycomb Repressive Complex 2) component known to be linked to lncRNAs and to epigenetically regulates target genes. By using SUZ12 RNA Immunoprecipitation, we identify one lncRNA named XLOC_087120 linked to SUZ12. XLOC_087120 is located in a region enriched in histone genes. Pearson correlation showed a significative anti-correlation between XLOC_087120 and histone neighboring coding gene expression suggesting a role of this lncRNA in the regulation of histone genes. The impact on histone genes expression was confirmed by overexpression and inhibition of XLOC_087120 in AML cell lines. Overexpression of NPM1 mutant in an AML cell line showed that NPM1 modulates the nuclear/cytoplasmic localization of XLOC_087120 and consequently its repressive function. Altogether, these data suggest that lncRNAs should be considered as key players in the pathogenesis of acute myeloid leukemias.

Mon travail de thèse porte sur l’étude du rôle de l’histone acétyl-transférase MOZ et de l’histone méthyle-transférase MLL dans l’hématopoïèse. Elles contrôlent l’expression de nombreux gènes, nottament des gènes HOX, des facteurs de transcription connus pour leur rôle dans l’hématopoïèse normale et pathologique. Les deux protéines ont des gènes cibles communs tel qu'HOXA9. Ces observations nous ont conduit à rechercher une coopération fonctionnelle entre MOZ et MLL. Nous avons montré que MOZ était associée avec MLL dans les cellules souches/progénitrices humaines CD34+ afin d’activer la transcription des gènes HOXA5, HOXA7 et HOXA9. En effet, les deux protéines interagissent et sont recrutées au niveau de leur promoteur. Nous avons mis en évidence une interférence fonctionnelle entre ces deux facteurs épigénétiques, puisque MOZ est nécessaire au recrutement et à l’activité enzymatique de MLL au niveau des gènes HOXA5, HOXA7 et HOXA9 et réciproquement.Afin de caractériser le mécanisme d’action impliquant la coopération entre MOZ et MLL, nous avons recherché d’autres partenaires associés à ce duo. Nous avons identifié la Symplekin, un membre de la machinerie de polyadénylation. Nous avons mis en évidence l’interaction de la Symplekin avec MOZ et MLL dans les cellules de la lignée hématopoïétique humaine KG1. Les trois protéines sont co-recrutées sur le promoteur du gène HOXA9. Nous avons démontré le rôle ambivalent de la Symplekin. Bien qu’elle soit importante pour la polyadénylation et par conséquent pour la stabilité de l’ARN Hoxa9, la Symplekin empêche le recrutement de MOZ et de MLL au niveau du gène HOXA9, conduisant ainsi à une diminution de sa transcription. / My thesis project has consisted of the study of MOZ, and MLL. They are epigenetic regulators. MOZ and MLL activate transcription of HOX genes, which are transcription factors essential during haematopoiesis. MOZ and MLL have some target genes in common. In our study, we characterised a cooperation between MOZ and MLL in human haematopoietic stem/progenitor cells CD34+. They are both recruited onto HOX promoters. MOZ is essential for MLL recruitment, and this is reciprocal. In conclusion, we provided an example of a mechanism involving a direct cross-talk between two histone modifying enzymes.In order to dissect the mechanism of action of this complex, we decided to identify novel proteins interacting with both MOZ and MLL. A member of the RNA polyadenylation machinery has been isolated: Symplekin. We confirmed the interaction between MOZ, MLL and Symplekin in the human haematopoietic immature cell line KG1. We showed that Symplekin is co-recruited to HOXA9 promoter along with MOZ and MLL. We demonstrated the dual role of this member of the polyadenylation machinery. Indeed, besides the fact that Symplekin is important for Hoxa9 polyadenylation, thus its stability, it prevents MOZ and MLL recruitment onto HOXA9 promoter, leading to a decrease of HOXA9 transcription.Our work improved the understanding of the mechanism of action of MOZ and MLL in HOX control.

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