Orientador: Maeli Dal-Pai / Resumo: Em mamíferos, a miogênese é o processo de desenvolvimento embrionário do tecido muscular que, a nível molecular, é regulado pela interação de transdutores de sinais intracelulares e fatores de transcrição nucleares. Durante o desenvolvimento do músculo esquelético, as células dos somitos comprometem-se à linhagem miogênica e progridem ao longo da via miogênica através de eventos celulares de proliferação e diferenciação terminal e, posteriormente, formação das miofibras multinucleadas. Durante esses processos, há a ativação dos fatores de regulação miogênicos (MRFs), resultando numa reprogramação da expressão gênica responsável pelo orquestramento da miogênese esquelética. Os MRFs são importantes para o desenvolvimento muscular, porém eles não explicam por si só o sofisticado padrão gênico de expressão durante a miogênese. A Osteoglicina (OGN) faz parte dos pequenos proteoglicanos que são secretados pela matriz extracelular e que apresenta expressão gênica alterada durante o processo de miogênese. Embora a OGN já tenha sido identificada como parte do secretoma de células musculares, ainda não foi avaliada a sua função nos processos de proliferação, migração e diferenciação de células musculares. A complexidade dos mecanismos de controle da expressão gênica nesse processo sugere o envolvimento de moléculas reguladoras adicionais, como os micro-RNAs; essas moléculas de RNA codificadas pelo genoma regulam vários processos celulares do músculo esquelético e estão envolvidas em vá... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In mammals, myogenesis is the process of embryonic development of muscle tissue at the molecular level that is regulated by interaction of intracellular signal transducers and nuclear transcription factors. Somite cells are committed to the myogenic lineage and progress along the development of muscle cells and subsequently formation of multinucleated myofiber. During these processes there is the activation of Myogenic Regulatory Factors (MRFs), resulting in a reprogramming of gene expression responsible for the control of skeletal myogenesis. MRFs are important for muscle development, but they do not explain by themselves the sophisticated pattern of gene expression during myogenesis. The Osteoglycin (OGN) is part of the small proteoglycans that are secreted by the extracellular matrix and presenting gene expression changes during the myogenesis process. Although OGN has been identified as part of the muscle cell secretome, it has not been rated it role in proliferation, migration and, differentiation of muscle cells. The complexity of the control mechanisms of gene expression in this process suggests the involvement of additional regulatory molecules, such as micro-RNAs. These RNA molecules encoded by the genome regulate various cellular processes in skeletal muscle and are involved in various diseases. Micro-RNAs work in order to control a common biological pathway or function. Using computer algorithms, we found miR-22 as an important candidate for post-transcriptional re... (Complete abstract click electronic access below) / Mestre

MicroRNAs are small non-coding RNAs which regulate gene expression by binding to 3&rsquo / UTR of their target mRNAs. Deregulated expression of microRNAs is detected in many pathologies including different types of cancers. miR-106b, is a member of miR-106b-25 cluster and overexpressed in many cancers including breast cancer. Based on miR-106b overexpression, we hypothesized that miR-106b may be an oncogene candidate. To explore miR-106b related phenotypes, we used an already miR-106b transfected model cell line system. Stably transfected MCF10A cells were investigated for alterations in cell growth, motility, migration and invasion. Our results showed that miR-106b overexpression caused increased growth motility and migration. On the other hand, based on matrigel invasion assay miR-106b expression caused a reduction in cell invasion. Further studies are needed to be performed to understand the precise role of miR-106b in breast cancer. Studies are underway to detect possible miR-106b targets that may help to explain these phenotypical alterations.

Genomic instability is commonly seen in breast cancers. To date, various chromosomal or segmental loss or amplification regions have been detected in primary tumors and cell lines. Hence, an intensive search for potent tumor suppressors or oncogenes located in these regions continues. MicroRNAs (miRNAs) are ~18-24 nt long non-coding RNAs that regulate protein expression either by target mRNA cleavage or translational repression. We hypothesized that miRNAs located in genomic instability regions in breast cancer cells may contribute to the initiation or maintenance of breast tumors. Here, we investigated genomic levels of miRNAs on frequent loss or gain regions of breast cancer cells. First, using bioinformatics resources we mapped known miRNAs and candidate miRNAs to reported genomic instability regions. Our extensive searches resulted with more than 30 known miRNAs and 35 candidate miRNAs. To further confirm loss or amplification of miRNA genes on these chromosomal regions in breast cancer cells, we designed specific primers for the known pre-miRNA DNA regions and performed semi-quantitative PCR in 20 breast cancer cell lines, 2 immortalized mammary cell lines, and 2 control samples. Densitometry results suggested that a striking 61 % (22/36) of selected miRNAs showed either loss or amplification in at least 3 different breast cancer cell lines. Interestingly most of these alterations were found to be amplifications even in regions reported to harbor losses in breast tumors. Genomic fold change results of these microRNAs provide a biologically relevant starting point for further expression and functional experiments of microRNAs in breast cancer studies. Genomic fold change analysis followed expression analysis of two significant microRNAs (hsa-miR-21 and hsa-miR-383) was done by qRT-PCR method. Our data provide a wide screen of genomic instability of 36 microRNA genes in 20 breast cancer cells and normal samples detected by semi-quantitative duplex PCR method as well as expression analysis of two microRNAs. To this date, such an extensive data on genomic status of microRNA genes in breast cancer cells did not exist. Therefore, our results are the first comprehensive investigation of many microRNA genes on genomic instability regions in breast cancers and provide further clues to the potential involvement of these microRNAs in breast tumorigenesis MicroRNA genomic instability may affect their expression and therefore their targets&rsquo / expressions. Understanding how these microRNAs regulate their targets and contribute to the neoplastic events will also contribute to the field by using this information for future diagnostic and threaupetical applications.

microRNA dependent gene expression regulation has roles in diverse processes such as differentiation, proliferation and apoptosis. Therefore, deregulated miRNA expression has functional importance for various diseases, including cancer. miR-125b is among the commonly downregulated miRNAs in breast cancer cells . Therefore we aimed to characterize the effects of miR-125b expression in MCF7 breast cancer cell line (BCCL) to better understand its roles in tumorigenesis. Here, we investigated mir-125 family members

Small RNAs (sRNAs), circa 21-26nt RNA molecules, are a novel class of regulatory molecules that influence many aspects of plant biology. The first objective of this thesis was to utilize computational approaches both to investigate how microRNAs (miRNAs), a type of sRNA, as a class affect their target transcripts’ accumulation and to identify novel miRNAs in Arabidopsis thaliana. The second objective of this thesis was to examine the regulation of protein coding (PC) cis natural antisense transcripts (cis-NATs), which have the potential to make double stranded RNA. Computational analysis of the expression of miRNA-regulated genes demonstrated that the transcriptomes of the inflorescences of plants defective in miRNA biogenesis were similar to normal leaf tissues and dissimilar to normal pollen and seed. Thus, miRNAs cause the plant transcriptome to shift from a vegetative to reproductive state. Known miRNA targets fail to explain miRNA-defective mutant transcriptome patterns. Novel computational approaches were used to discover five new mature miRNAs. Interestingly, two miRNAs have different functions but are encoded by perfect complements of the same precursor molecule. Genome-wide analysis of cis-NAT abundances revealed that protein coding (PC) cis-NATs tend to be co-expressed, broadly expressed, and highly expressed across diverse abiotic stress conditions. These expression patterns were negatively associated with sRNAs because sRNAs were under-represented within PC cis-NATs compared to PC non-cis-NATs. sRNAs also mapped to cis-NATs and non-cis-NATs at similar frequencies in mutants defective in nat-siRNA biogenesis relative to other genotypes. We suggest a common euchromatin environment and possibly antisense RNA stabilization of mRNA transcripts may contribute to the high level, breadth, and co-expression of cis-NATs. However, cis-NATs are correlated less frequently than expected, and cis-NAT transcript abundances often differ more than expected. In addition, sRNAs matched PC cis-NATs relative to PC non-cis-NATs more frequently in abiotic stress conditions than in control conditions. Thus, although sRNAs do not have a widespread role in regulating cis-NATs, sRNAs may have a focused role in regulating cis-NAT transcript abundances. / PhD thesis / NSERC

Recently, the importance of non-coding regions of the genome, which were once presumed to be “junk” DNA, has been revealed. The non-coding 3’ untranslated region (3’UTR) plays a significant role in the regulation of microRNA (miRNA) functions. The 3’UTR is hypothesized to function in the feed-back regulation of miRNA functions, since it can bind and inactivate multiple miRNAs. In this study, the effects of the exogenous over-expression of two 3’UTRs, CD44 and Tumour Suppressor candidate 2 (TUSC2), on miRNA functions in breast cancer carcinogenesis were investigated. A series of cell function assays in human and mouse breast cancer cell lines, MT-1, MDA-MB-231 and 4T1 showed phenotypic changes caused by the 3’UTRs. A variety of cell function characteristics were affected, including cell proliferation, colony formation, cell survival, angiogenesis, tumour growth, cell migration, invasion and adhesion. These results were hypothesized to occur due to the interaction of the 3’UTRs with multiple miRNAs. The 3’UTRs were able to antagonize cytoplasmic miRNAs, as demonstrated by luciferase activities. In the case of the CD44 3’UTR, downstream target mRNAs, CDC42, Col1a1 and FN1 had an increased expression along with CD44. When the 3’UTR of TUSC2 was over-expressed, there was an increased translation of TUSC2 and the downstream targets, tissue inhibitor of metalloproteinases (TIMP) -2 and -3.The 3’UTRs of these target mRNAs can bind and target multiple miRNAs in common with the TUSC2 3’UTR, which were confirmed with luciferase activity assays and correlated with a series of siRNA and miRNA assays. During the study of the TUSC2 3’UTR, a potential pseudogene, TUSC2P, was discovered. Interestingly, TUSC2P mRNA expression was found to be decreased in cancer cells compared to normal cells and had similar cell functional characteristics as that of the TUSC2 3’UTR. These findings suggest that the over-expressed non-coding transcript can serve as a competitor for miRNA binding, which freed the potential targets of the miRNAs and led to an up-regulation of multiple protein levels. The non-coding transcript can thus be used as a functional miRNA inhibitor that is capable of modulating multiple miRNAs, which can be applied towards treating cancer in the form of gene therapy.

Recently, the importance of non-coding regions of the genome, which were once presumed to be “junk” DNA, has been revealed. The non-coding 3’ untranslated region (3’UTR) plays a significant role in the regulation of microRNA (miRNA) functions. The 3’UTR is hypothesized to function in the feed-back regulation of miRNA functions, since it can bind and inactivate multiple miRNAs. In this study, the effects of the exogenous over-expression of two 3’UTRs, CD44 and Tumour Suppressor candidate 2 (TUSC2), on miRNA functions in breast cancer carcinogenesis were investigated. A series of cell function assays in human and mouse breast cancer cell lines, MT-1, MDA-MB-231 and 4T1 showed phenotypic changes caused by the 3’UTRs. A variety of cell function characteristics were affected, including cell proliferation, colony formation, cell survival, angiogenesis, tumour growth, cell migration, invasion and adhesion. These results were hypothesized to occur due to the interaction of the 3’UTRs with multiple miRNAs. The 3’UTRs were able to antagonize cytoplasmic miRNAs, as demonstrated by luciferase activities. In the case of the CD44 3’UTR, downstream target mRNAs, CDC42, Col1a1 and FN1 had an increased expression along with CD44. When the 3’UTR of TUSC2 was over-expressed, there was an increased translation of TUSC2 and the downstream targets, tissue inhibitor of metalloproteinases (TIMP) -2 and -3.The 3’UTRs of these target mRNAs can bind and target multiple miRNAs in common with the TUSC2 3’UTR, which were confirmed with luciferase activity assays and correlated with a series of siRNA and miRNA assays. During the study of the TUSC2 3’UTR, a potential pseudogene, TUSC2P, was discovered. Interestingly, TUSC2P mRNA expression was found to be decreased in cancer cells compared to normal cells and had similar cell functional characteristics as that of the TUSC2 3’UTR. These findings suggest that the over-expressed non-coding transcript can serve as a competitor for miRNA binding, which freed the potential targets of the miRNAs and led to an up-regulation of multiple protein levels. The non-coding transcript can thus be used as a functional miRNA inhibitor that is capable of modulating multiple miRNAs, which can be applied towards treating cancer in the form of gene therapy.

High expression levels of the gene BAALC (brain and acute leukemia, cytoplasmic) are associated with poor prognosis in acute myeloid leukemia (AML) patients, but the underlying mechanisms are not yet understood. We evaluated the prognostic significance of expression levels of miR-3151, a newly discovered microRNA embedded in intron 1 of the BAALC gene, in a cohort of 179 older (≥60 years) cytogenetically normal AML (CN-AML) patients, in the context of established molecular markers and especially with regard to the possible interplay with its host gene BAALC. In multivariable analyses, high miR-3151 was associated with shorter disease-free and overall survival (OS), while higher BAALC expression strongly predicted failure of complete remission attainment and OS. Patients exhibiting both high miR-3151 and BAALC expression had worse outcome than patients expressing low levels of either one of the genes or both. Next, gene - and microRNA-expression profiles associated with miR-3151 expression were derived using microarrays, and a pathway analysis of the miR-3151 associated gene signature was performed using Ingenuity software. High miR-3151 expressers showed downregulation of genes involved in transcriptional regulation, post-translational modifications and cell-cycle control. Two genes of the ubiquitination pathway, FBXL20 and USP40, were experimentally validated as direct miR-3151 targets. In summary, we identified high expression levels of the intronic miR-3151 as a novel, independent prognosticator for poor outcome in CN-AML. Interestingly, miR-3151 impacted differently on outcome than its host gene BAALC; and the combination of both markers identified a patient subset with the poorest outcome, suggesting that the microRNA and its host gene contribute to clinical and prognostic features of CN-AML independently and through distinct mechanisms. This is the first example of the interplay of an intronic miR and its host gene in leukemia. Its discovery may have important biologic implications for future targeted treatment strategies.

Orientador: Ana Marisa Fusco-Almeida / Coorientador: Francisco Javier Enguita / Banca: Eloisa aparecida Mocheuti Kronka / Banca: Daniel Guariz Pinheiro / Banca: Eleini Gomes / Banca: Tais Maria Bauab / Resumo: O processo de fermentação é amplamente utilizado em usinas brasileiras para produção de bioetanol e, mesmo sendo um processo amplamente difundido, a problemática sobre contaminações por micro-organismos ainda é uma incógnita. Problemas de redução de produtividade estão diretamente ligados à competição de nutrientes quando há decorrentes crises de contaminações por bactérias e leveduras não-Saccharomyces. Entre as leveduras contaminantes mais encontradas estão as pertencentes aos gêneros Candida, Torulopis, Rhodotorula, Pichia, Komagataella e Schizosaccharomyces. Muitos antimicrobianos são utilizados para combater contaminações, porém com baixas especificidade e eficiência para leveduras contaminantes. O desenvolvimento de novas alternativas para a descontaminação do processo fermentativo e a busca por biomoléculas naturais e não geradoras de resíduos tóxicos, são emergenciais. Tais biomoléculas podem ser originárias dos miRNAs, que são pequenas moléculas de RNA não codificantes que afetam a estabilidade dos RNAs mensageiros, atuando na expressão de transcritos dentro de processos biológicos, afetando controles transcricionais e pós-transcricionais, resultando na inibição ou potencialização da ação gênica nos processos biológicos fermentativos. Dessa forma, miRNAs livres na dorna de fermentação podem interferir de maneira controlada os contaminantes que competem com a levedura Saccharomyces cerevisiae na produção de bioetanol. Em estudos anteriores de nosso grupo foi seleciona... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The fermentation process is widely used in Brazilian plants for the production of bioethanol and, even though it is a widely diffused process, the problem of contamination by microorganisms is still unknown. Productivity reduction problems are directly linked to nutrient competition when there are bouts of contamination by bacteria and non-Saccharomyces yeasts. Among the most common contaminating yeasts are those belonging to the genera Candida, Torulopis, Rhodotorula, Pichia, Komagataella and Schizosaccharomyces. Many antimicrobials are used to combat contamination, but with low specificity and efficiency for contaminating yeasts. The development of new alternatives for the decontamination of the fermentative process and the search for natural biomolecules and non-toxic wastes are emergency. Such biomolecules may originate from the miRNAs, which are small molecules of non-coding RNA that affect the stability of messenger RNAs, acting on the expression of transcripts within biological processes, affecting transcriptional and post-transcriptional controls, resulting in the inhibition or potentiation of the gene action fermentative biological processes. Thus, free miRNAs in the fermentation dorna can interfere in a controlled manner the contaminants that compete with the yeast Saccharomyces cerevisiae in the production of bioethanol. In previous studies of our group, a contaminant strain of Candida tropicalis, isolated from a plant in the region of Araraquara/SP, was selected and studied, which persevered during the period of one harvest. As a continuity, our study aimed to elucidate the metabolic and transcriptional behavior of the relevant contaminant, C. tropicalis, during the fermentation cycle, through fermentative capacity techniques, sequencing of global RNA and to identify target genes for the development of miRNAs as antifungal biomolecules... (Complete abstract click electronic access below) / Doutor

Orientador: Cesar Martins / Resumo: Cromossomos supernumerários são polimorfismos numéricos frequentemente registrados em eucariotos, sendo que seus efeitos são pouco elucidados. Em alguns indivíduos da espécie Astatotilapia latifasciata pode-se identificar um ou dois cromossomos B, que são totalmente heterocromáticos e ricos em sequências repetitivas. Em vista de compreender sua origem, evolução e efeitos, este elemento vem sendo largamente explorado por técnicas integradas de citogenética, biologia molecular e genômica. Aqui, explorou-se o padrão de marcas epigenéticas do DNA deste cromossomo B e seus efeitos nas vias de metilação do DNA e de formação de tRFs. Usando-se imunocitogenética, ferramentas de bioinformática, quantificação global de 5mC e 5hmC e RT-qPCR, identificou-se que o cromossomo B de A. latifasciata possui padrão epigenético ativo e que não é um isocromossomo. Além disso, foram observados efeitos heterogêneos deste cromossomo na expressão de epi-miRNAs candidatos, de genes de modificações epigenéticas do DNA e de genes relacionados com a formação de tRFs. Como consequência, também foram registrados efeitos de cromossomos B nos níveis globais de 5mC e 5hmC e na formação de tRFs. Essas variações observadas parecem estar relacionadas com os mecanismos de manutenção do cromossomo B e estão em desacordo com a difundida ideia de que ele seja um elemento inerte. / Doutor