The detection of non-protein-coding RNA (ncRNA) genes in bacteria and their diverse regulatory mode of action moved the experimental and bio-computational analysis of ncRNAs into the focus of attention. Regulatory ncRNA transcripts are not translated to proteins but function directly on the RNA level. These typically small RNAs have been found to be involved in diverse processes such as (post-)transcriptional regulation and modification, translation, protein translocation, protein degradation and sequestration. Bacterial ncRNAs either arise from independent primary transcripts or their mature sequence is generated via processing from a precursor. Besides these autonomous transcripts, RNA regulators (e.g. riboswitches and RNA thermometers) also form chimera with protein-coding sequences. These structured regulatory elements are encoded within the messenger RNA and directly regulate the expression of their “host” gene. The quality and completeness of genome annotation is essential for all subsequent analyses. In contrast to protein-coding genes ncRNAs lack clear statistical signals on the sequence level. Thus, sophisticated tools have been developed to automatically identify ncRNA genes. Unfortunately, these tools are not part of generic genome annotation pipelines and therefore computational searches for known ncRNA genes are the starting point of each study. Moreover, prokaryotic genome annotation lacks essential features of protein-coding genes. Many known ncRNAs regulate translation via base-pairing to the 5’ UTR (untranslated region) of mRNA transcripts. Eukaryotic 5’ UTRs have been routinely annotated by sequencing of ESTs (expressed sequence tags) for more than a decade. Only recently, experimental setups have been developed to systematically identify these elements on a genome-wide scale in prokaryotes. The first part of this thesis, describes three experimental surveys of exploratory field studies to analyze transcript organization in pathogenic bacteria. To identify ncRNAs in Pseudomonas aeruginosa we used a combination of an experimental RNomics approach and ncRNA prediction. Besides already known ncRNAs we identified and validated the expression of six novel RNA genes. Global detection of transcripts by next generation RNA sequencing techniques unraveled an unexpectedly complex transcript organization in many bacteria. These ultra high-throughput methods give us the appealing opportunity to analyze the complete RNA output of any species at once. The development of the differential RNA sequencing (dRNA-seq) approach enabled us to analyze the primary transcriptome of Helicobacter pylori and Xanthomonas campestris. For the first time we generated a comprehensive and precise transcription start site (TSS) map for both species and provide a general framework for the analysis of dRNA-seq data. Focusing on computer-aided analysis we developed new tools to annotate TSS, detect small protein-coding genes and to infer homology of newly detected transcripts. We discovered hundreds of TSS in intergenic regions, upstream of protein-coding genes, within operons and antisense to annotated genes. Analysis of 5’ UTRs (spanning from the TSS to the start codon of the adjacent protein-coding gene) revealed an unexpected size diversity ranging from zero to several hundred nucleotides. We identified and validated the expression of about 60 and about 20 ncRNA candidates in Helicobacter and Xanthomonas, respectively. Among these ncRNA candidates we found several small protein-coding genes that have previously evaded annotation in both species. We showed that the combination of dRNA-seq and computational analysis is a powerful method to examine prokaryotic transcriptomes. Experimental setups are time consuming and often combined with huge costs. Another limitation of experimental approaches is that genes which are expressed in specific developmental stages or stress conditions are likely to be missed. Bioinformatic tools build an alternative to overcome such restraints. General approaches usually depend on comparative genomic data and evolutionary signatures are used to analyze the (non-)coding potential of multiple sequence alignments. In the second part of my thesis we present our major update of the widely used ncRNA gene finder RNAz and introduce RNAcode, an efficient tool to asses local protein-coding potential of genomic regions. RNAz has been successfully used to identify structured RNA elements in all domains of life. However, our own experience and the user feedback not only demonstrated the applicability of the RNAz approach, but also helped us to identify limitations of the current implementation. Using a much larger training set and a new classification model we significantly improved the prediction accuracy of RNAz. During transcriptome analysis we repeatedly identified small protein-coding genes that have not been annotated so far. Only a few of those genes are known to date and standard proteincoding gene finding tools suffer from the lack of training data. To avoid an excess of false positive predictions, gene finding software is usually run with an arbitrary cutoff of 40-50 amino acids and therefore misses the small sized protein-coding genes. We have implemented RNAcode which is optimized for emerging applications not covered by standard protein-coding gene annotation software. In addition to complementing classical protein gene annotation, a major field of application of RNAcode is the functional classification of transcribed regions. RNA sequencing analyses are likely to falsely report transcript fragments (e.g. mRNA degradation products) as non-coding. Hence, an evaluation of the protein-coding potential of these fragments is an essential task. RNAcode reports local regions of high coding potential instead of complete protein-coding genes. A training on known protein-coding sequences is not necessary and RNAcode can therefore be applied to any species. We showed this with our analysis of the Escherichia coli genome where the current annotation could be accurately reproduced. We furthermore identified novel small protein-coding genes with RNAcode in this extensively studied genome. Using transcriptome and proteome data we found compelling evidence that several of the identified candidates are bona fide proteins. In summary, this thesis clearly demonstrates that bioinformatic methods are mandatory to analyze the huge amount of transcriptome data and to identify novel (non-)coding RNA genes. With the major update of RNAz and the implementation of RNAcode we contributed to complete the repertoire of gene finding software which will help to unearth hidden treasures of the RNA World.

Em procariotos, RNAs antisense (asRNAs) constituem a classe de RNAs não codificantes (ncRNAs) mais numerosa detectada por métodos de avaliação de transcritoma em larga escala. Apesar da grande abundância, pouco se sabe sobre mecanismos regulatórios e aspectos da conservação evolutiva dessas moléculas, principalmente em arquéias, onde o mecanismo de degradação de RNAs dupla fita (dsRNAs) é um fenômeno pouco conhecido. No presente estudo, utilizando dados de dRNA-seq, identificamos 1626 inícios de transcrição primários antisense (aTSSs) no genoma de Halobacterium salinarum NRC-1, importante organismo modelo para estudos de regulação gênica no domínio Archaea. Integrando dados de expressão gênica obtidos a partir de 18 bibliotecas de RNA-seq paired-end, anotamos 846 asRNAs a partir dos aTSSs mapeados. Encontramos asRNAs em ~21% dos genes anotados, alguns desses relacionados a importantes características desse organismo como: codificadores de proteínas que constituem vesículas de gás e da proteína bacteriorodopsina, além de vários genes relacionados a maquinaria de tradução e transposases. Além desses, encontramos asRNAs em genes pertencentes a sistemas de toxinas-antitoxinas do tipo II e utilizando dados públicos de dRNA-seq, evidenciamos que esse é um fenômeno que ocorre em bactérias e arquéias. A interação de um ncRNA com seu RNA alvo pode ser dependente de proteínas, em arquéias, a proteína LSm é uma chaperona de RNA homóloga a Hfq de bactérias, implicada no controle pós-transcricional. Utilizamos dados de RIP-seq de RNAs imunoprecipitados com LSm e identificamos 91 asRNAs interagindo com essa proteína, para 81 desses, o mRNA do gene sense também foi encontrado interagindo. Buscando por aTSSs presentes nas mesmas regiões de genes ortólogos, identificamos 160 aTSSs que dão origem a asRNAs em H. salinarum possivelmente conservados em Haloferax volcanii. A expressão dos asRNAs anotados foi avaliada ao longo de uma curva de crescimento e em uma linhagem knockout de um gene que codifica uma RNase R, possível degradadora de dsRNAs em arquéias. Encontramos um total de 144 asRNAs diferencialmente expressos ao longo da curva de crescimento, para 56 desses o gene sense também está diferencialmente expresso, caracterizando possíveis mecanismos de regulação em cis por esses RNAs. Na linhagem knockout, encontramos cinco asRNAs diferencialmente expressos e apenas para um desses o gene sense também está diferencialmente expresso, resultado que não nos permitiu inferir um possível papel de degradação de dsRNAs da RNAse R em H. salinarum NRC-1. Nesse trabalho apresentamos um mapeamento completo do transcritoma antisense primário de H. salinarum NRC-1 com resultados que consistem em um importante passo na direção da compreensão do envolvimento da transcrição antisense na regulação gênica pós-transcricional desse organismo modelo do terceiro domínio da vida. / Antisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.

Em procariotos, RNAs antisense (asRNAs) constituem a classe de RNAs não codificantes (ncRNAs) mais numerosa detectada por métodos de avaliação de transcritoma em larga escala. Apesar da grande abundância, pouco se sabe sobre mecanismos regulatórios e aspectos da conservação evolutiva dessas moléculas, principalmente em arquéias, onde o mecanismo de degradação de RNAs dupla fita (dsRNAs) é um fenômeno pouco conhecido. No presente estudo, utilizando dados de dRNA-seq, identificamos 1626 inícios de transcrição primários antisense (aTSSs) no genoma de Halobacterium salinarum NRC-1, importante organismo modelo para estudos de regulação gênica no domínio Archaea. Integrando dados de expressão gênica obtidos a partir de 18 bibliotecas de RNA-seq paired-end, anotamos 846 asRNAs a partir dos aTSSs mapeados. Encontramos asRNAs em ~21% dos genes anotados, alguns desses relacionados a importantes características desse organismo como: codificadores de proteínas que constituem vesículas de gás e da proteína bacteriorodopsina, além de vários genes relacionados a maquinaria de tradução e transposases. Além desses, encontramos asRNAs em genes pertencentes a sistemas de toxinas-antitoxinas do tipo II e utilizando dados públicos de dRNA-seq, evidenciamos que esse é um fenômeno que ocorre em bactérias e arquéias. A interação de um ncRNA com seu RNA alvo pode ser dependente de proteínas, em arquéias, a proteína LSm é uma chaperona de RNA homóloga a Hfq de bactérias, implicada no controle pós-transcricional. Utilizamos dados de RIP-seq de RNAs imunoprecipitados com LSm e identificamos 91 asRNAs interagindo com essa proteína, para 81 desses, o mRNA do gene sense também foi encontrado interagindo. Buscando por aTSSs presentes nas mesmas regiões de genes ortólogos, identificamos 160 aTSSs que dão origem a asRNAs em H. salinarum possivelmente conservados em Haloferax volcanii. A expressão dos asRNAs anotados foi avaliada ao longo de uma curva de crescimento e em uma linhagem knockout de um gene que codifica uma RNase R, possível degradadora de dsRNAs em arquéias. Encontramos um total de 144 asRNAs diferencialmente expressos ao longo da curva de crescimento, para 56 desses o gene sense também está diferencialmente expresso, caracterizando possíveis mecanismos de regulação em cis por esses RNAs. Na linhagem knockout, encontramos cinco asRNAs diferencialmente expressos e apenas para um desses o gene sense também está diferencialmente expresso, resultado que não nos permitiu inferir um possível papel de degradação de dsRNAs da RNAse R em H. salinarum NRC-1. Nesse trabalho apresentamos um mapeamento completo do transcritoma antisense primário de H. salinarum NRC-1 com resultados que consistem em um importante passo na direção da compreensão do envolvimento da transcrição antisense na regulação gênica pós-transcricional desse organismo modelo do terceiro domínio da vida. / Antisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.

Das Leben auf der Erde wird maßgeblich durch die Kraft der oxygenen Photosythese bestimmt, die Sonnen- in chemische Energie umwandelt. Cyanobakterien wie Prochloro- und Synechococcus zählen zu den wichtigsten primären Produzenten der Ozeane und werden zunehmend als Modelle für photosynthetische Organismen genutzt. Um die Regulationsmechanismen dieser Picocyanobakterien besser zu verstehen, wurde hier die Information von vier Genomen hochgradig verwandter aber dennoch ökologisch unterschiedlich angepasster mariner Stämme genutzt in einer Kombination aus computer-gestützten und experimentellen Untersuchungen. Sequenzsignale und RNA-kodierende Gene wurden als neuartige Regulationselemente identifiziert und entlang des phylogenetischen Gradienten verglichen. Mittels ''phylogenetic footprinting'' konnte ein minimales, konserviertes Set möglicher Transkriptionsfaktoren, deren Bindestellen und Regulons aufgedeckt werden. NtcA-, LexA- und ArsR-ähnliche Motive wurden ebenso gefunden wie neue regulatorische Elemente. Mit Hilfe von RACE Experimenten wurden einige der vorhergesagten Bindestellen Promotorregionen zugeordnet. Eine Suche nach konservierten Sekundärstrukturen detektierte mehrere nicht-kodierende RNAs, benannt Yfr für cYanobacterial Functional RNA. Eine vergleichende Analyse von Yfr7 innerhalb der cyanobakteriellen Linie ergab, dass diese RNA wahrscheinlich ein Homolog der E. coli 6S RNA ist. Zwei verschiedene Yfr7 Transkripte mit einem zirkadianen aber zeitversetzten Akkumulationsmuster lassen eine Verknüpfung ihrer Expression mit dem zirkadianen Rhythmus oder der Lichtintensität vermuten. Experimente in Synechocystis deckten einen neuartigen Regulationsmechanismus durch eine antisense RNA auf, welche die Menge der isiA mRNA kontrolliert und die Assemblierung von IsiA-Superkomplexen beeinflusst. Die funktionelle Zuordnung dieser neuen Elemente wird zu einem besseren Verständnis regulatorischer Netzwerke in marinen Cyanobakterien und darüber hinaus führen. / Life on Earth is driven by the power of oxygenic photosynthesis transforming solar into chemical energy. Cyanobacteria such as Prochlorococcus and Synechococcus belong to the most important primary producers within the oceans and increasingly serve as models for photosynthetic organisms. To better understand the regulatory mechanisms in these picocyanobacteria, here the information from four genomes of closely related and even so ecologically divergent marine strains was used in a combined computational and experimental approach. Sequence signals and RNA-coding genes as novel elements in the regulation of gene expression were identified and their distribution along the phylogenetic gradient compared. Phylogenetic footprinting revealed a minimal conserved set of putative transcription factors, their binding sites and regulons. Sites for NtcA, LexA and ArsR-like regulators were found as well as new cis elements. RACE experiments verified several of these predicted sites belonging to the promoter region. A search, focussing on conserved secondary structures, detected several non-coding RNAs named Yfr for cYanobacterial Functional RNA. A comparative analysis of Yfr7 structures, transcript types and accumulation throughout the cyanobacterial radiation indicated this RNA as the likely homologue of the E. coli 6S RNA. Two distinct Yfr7 transcripts with a circadian but time-shifted expression pattern suggested a coupling of their expression to the circadian rhythm or light intensity. Experiments in Synechocystis discovered a novel antisense RNA-mediated regulatory mechanism that controls isiA mRNA abundance and assembly of IsiA-photosystem I supercomplexes. Functional assignments of these new elements in the future will contribute to a deeper understanding of the regulatory network of marine cyanobacteria and promote new studies on bacterial ncRNAs.

Introdução: Os micro RNA (miRNA) são formados a partir de RNA precursores de fita dupla que contém entre 60 a 110 nucleotídeos e formam estruturas do tipo hairpin. Imediatamente após sua transcrição pela RNA polimerase II a enzima Dicer promove a clivagem do RNA precursor em seqüências menores contendo 19 a 22 nucleotídeos. Após a clivagem, o miRNA integra-se ao complexo silenciador induzido pelo RNA (RISC) que o conduz ao seu RNA mensageiro (mRNA) homólogo recém transcrito. Esta associação promove a degradação do mRNA, ou interfere na tradução da proteína caracterizando um grande mecanismo de controle da expressão dos genes. Este mecanismo está relacionado ao desenvolvimento de órgãos e tecidos, e está envolvido no processo de carcinogênese. Nosso objetivo é identificar um perfil de expressão de miRNA que defina o adenocarcinoma de próstata de prognóstico favorável e desfavorável considerando os níveis de PSA e dados anatomopatológicos. Materiais e métodos: Foram selecionados 53 pacientes com tumores desfavoráveis (mediana do escore de Gleason igual a 8, 79,2% estadiados pT3, mediana de PSA 10,1 ng/mL e mediana do volume tumoral de 23%) e 45 considerados favoráveis (mediana do escore de Gleason igual a 5, 80% estadiados pT2, mediana de PSA de 7,8 ng/mL e mediana do volume tumoral de 11,5%). O controle foi representado por 7 pacientes com hiperplasia prostática benigna (HPB). Todos os pacientes foram submetidos a prostatectomia radical pelo mesmo cirurgião. Os espécimes cirúrgicos foram examinados na sua totalidade pelo mesmo patologista. A análise dos miRNA foi feita a partir de tecido congelado e tecido incluído em parafina usando a técnica da reação em cadeia da polimerase em tempo real quantitativa (qRT-PCR) utilizando primers e sondas Taqman® específicas. O RNU43 foi usado como controle interno. Resultados: Com exceção dos miRNA 199a, 21, 15a, 16 e 25 que se mostraram subexpressos tanto nos casos desfavoráveis como nos favoráveis, houve uma diminuição global na expressão dos miRNA com redução estatisticamente significativa na expressão dos miRNA 143, 145 e 146a, 191, 218 e Let7c em tumores desfavoráveis em relação aos tumores favoráveis. Conclusão: Demonstramos que no processo de transição entre os carcinomas favoráveis e desfavoráveis de próstata existe uma perda global na expressão de miRNA que podem ser importantes controladores de expressão de uma série de genes relacionados a progressão desta neoplasia. Dados experimentais avaliando o papel desses miRNA devem ser conduzidos para que possamos definir seu papel na evolução do câncer de próstata / Introduction: micro RNA (miRNA) are formed from double-stranded RNA precursors that contain between 60-110 nucleotides and form structures such as hairpin. Immediately after their transcription by RNA polymerase II, the enzyme Dicer promotes the cleavage of precursor RNA sequences containing minor 19-22 nucleotides. After cleavage, the miRNA is part of the RNA-induced silencing complex (RISC) that leads to its messenger RNA (mRNA) newly transcribed counterpart. This association promotes the degradation of mRNA, or interferes with the protein translation characterizing a great mechanism for controlling gene expression. This mechanism is related to the development of organs and tissues, and may be involved in the process of carcinogenesis. Our goal is to identify a miRNA expression profile that distinguishes prostate adenocarcinoma of favorable and unfavorable prognosis considering the PSA and pathological findings. Material and Methods: We studied 53 patients with tumors considered unfavorable (Median of Gleason score 8, 79.2% staged pT3, median of PSA 10.1 ng/mL and median of tumor volume of 23%) and 45 considered favorable (Median of Gleason score 5, 80% staged pT2, median of PSA 7.8 ng/mL and median of tumor volume of 11.5%). The control group was represented by seven patients with benign prostatic hyperplasia (BPH). All patients underwent radical prostatectomy by the same surgeon. The surgical specimen was examined entirely by the same pathologist. The analysis of miRNA was made from frozen and paraffin embedded tissue by quantitative real-time polymerase chain reaction (qRT-PCR) using the Taqman® specific primers and probes. The RNU43 was used as a internal control. Results: Except for miRNAs 199a, 21, 15a, 16 e 25 that were underexpressed by both favorable and unfavorable prostate cancer, there was a global decrease of all miRNAs studied, and some differences were statistically significant as miRNAs 143, 145 e 146a, 191, 218 e Let7c that were underexpressed in unfavorable carcinomas compared favorable tumor. Conclusion: We have demonstrated that in the process of transition between favorable and unfavorable prostate cancer there is a global loss of expression of miRNAs. These molecules can be important controllers of a series of genes related to cancer progression. Experimental studies are needed in order to comprehend the role of these genes in prostate carcinogenesis

RNAs não codificadores longos (lncRNAs) compõem uma fração significativa do transcriptoma. Alterações na expressão de lncRNAs já foram observadas em vários cânceres humanos, mas ainda não foram exploradas no adenocarcinoma pancreático ductal (PDAC), uma doença devastadora e agressiva para a qual faltam métodos para diagnóstico precoce e tratamentos efetivos. Utilizando uma plataforma de microarranjo de cDNA com sondas para 984 lncRNAs e 2371 mRNAs, o presente estudo identificou conjuntos de lncRNAs expressos em 38 amostras clínicas pancreáticas. O enriquecimento de (i) elementos regulatórios associados às regiões promotoras (H3K4me3); (ii) possíveis inícios de transcrição (CAGE-tags); (iii) presença de elementos conservados sugere que ao menos uma fração desses RNAs seja originada a partir de unidades transcricionais independentes, reguladas e possivelmente funcionais. Foram identificadas assinaturas de expressão gênica compostas por mRNA e lncRNAs associadas ao tumor primário e à metástase pancreática. A assinatura gIenica associada à metástase apresentou enriquecimento RNAs intrônicos de loci gênicos associados à via MAPK quinase. O aumento de expressão dos transcritos intrônicos dos loci PPP3CB, MAP3K14 e DAPK1 foi confirmado por qPCR em metástases. Em conjunto, este trabalho aponta para a importância de lncRNAs intrônicos no PDAC e para a necessidade de estudos mais aprofundados para uma melhor compreensão do papel dessa classe de transcritos na biologia da doença. / Long noncoding RNAs (lncRNAs) compose a significant fraction of transcriptome. Altered expression of lncRNAs has been observed in diverse human cancers, but has not being investigated in pancreatic ductal adenocarcinoma (PDAC), a devastating and aggressive disease that lack early diagnosis methods and effective treatments. Using a cDNA microarray platform with probes interrogating 984 lncRNAs and 2371 mRNA, the present study identified subsets of lncRNAs expressed in 38 pancreatic clinical samples. Enrichment of (i) regulatory elements associated to promoter region (H3K4me3); (ii) putative transcription start site (CAGEtags) and (iii) conserved elements, suggest that at least a fraction of these RNAs could be independent transcriptional unit, regulated, an possibly functional. Gene expression signatures comprised of mRNAs and lncRNAs and associated to primary or metastatic tumors were found. A gene signature associated to metastasis was enriched in intronic ncRNAs mapping to gene loci associated to the MAPK pathway. Over expression of intronic RNAs from PPP3CB, MAP3K14 and DAPK1 was confirmed by qPCR in metastatic samples. Taken together, this study points to the importance of intronic lncRNAs in PDAC and for the need to study this class of ncRNAs in greater detail to better understand its role in the biology of PDAC.

O câncer de próstata é o quinto tipo mais comum de câncer no mundo e o mais comum em homens. Fatores clínicos e anatomopatológicos atualmente usados na clínica não são capazes de distinguir entre a doença indolente e a agressiva. Existe uma grande necessidade de novos marcadores de prognóstico, a fim de melhorar o gerenciamento clínico de pacientes de câncer de próstata. Além das anormalidades em genes codificadores de proteínas, alterações em RNAs não codificadores (ncRNAs) contribuem para a patogênese do câncer e, portanto, representam outra fonte potencial de biomarcadores de câncer de próstata. Entretanto, até o momento, poucos estudos de perfis de expressão de ncRNAs foram publicados. Este projeto teve como principal objetivo identificar perfis de expressão de genes codificadores e não codificadores de proteína correlacionados com recorrência de tumor de próstata, a fim de gerar um perfil prognóstico com potencial uso como biomarcadores e elucidar o possível papel de ncRNAs no desenvolvimento do câncer. Para isso, foram analisados os perfis de expressão de genes codificadores e não codificadores de proteína de um conjunto de 42 amostras de tecido tumoral de câncer de próstata de pacientes de amostras de pacientes submetidos à prostatectomia radical, com longo acompanhamento clínico (cinco anos) e conhecida evolução da doença Nós utilizamos microarranjos por nós desenhados e fabricados pela Agilent sob encomenda, interrogando aproximadamente 18.709 transcritos não codificadores longos (>500 nt), sem evidência de splicing, que mapeiam em regiões intrônicas dentro de 5.660 loci genômicos. Os dados de expressão foram extraídos de cada arranjo, normalizados entre todas as 42 amostras de pacientes. Usando uma estratégia de múltipla amostragem, foi identificado um perfil de expressão de mau prognóstico, contendo 51 transcritos intrônicos não codificadores de proteína. O perfil prognóstico de ncRNAs foi aplicado a um conjunto teste independente de 22 pacientes, classificando corretamente 82% das amostras. Uma análise de Kaplan-Meier dos pacientes do conjunto teste indicou que as curvas de sobrevida dos grupos de alto e baixo risco foram significativamente distintas (Log-rank test p = 0,0009; Hazard ratio = 23,4, 95% CI = 3,62 a 151,2), confirmando assim que este classificador é útil para identificar pacientes com alto risco de recorrência. Além disso, estas descobertas indicam um potencial papel destes RNAs intrônicos não codificadores na progressão do tumor de próstata e apontam para os RNAs intrônicos como potenciais novos marcadores de câncer / Prostate cancer is the fifth most common type of cancer in the world, and the most common in men. Clinical and anatomo-pathological factors currently used in clinic are not able to distinguish between the indolent and the aggressive disease. There is a major need of new prognostic makers in order to improve the clinical management of prostate cancer patients. Apart from abnormalities in protein-coding genes, changes in non-coding RNAs (ncRNAs) contribute to the pathogenesis of cancer and thus represent another potential source of prostate cancer biomarkers. However, few studies of expression profiles of ncRNAs have been published. This project aimed to identify expression profiles of protein-coding and non-coding genes correlated to prostate cancer biochemical recurrence. For this, we analyzed the expression profile of 42 prostate cancer samples from patients undergoing radical prostatectomy, with long follow-up (five years), and know disease outcome. We used a custom microarray designed by us and printed by Agilent, that probes 18,709 long (>500 nt) ncRNAs mapping to intronic regions within 5,660 genomic loci. The expression data were extracted from each array and normalized across all 42 samples. Using a multiple random sampling validation strategy, we identified an expression profile of poor prognosis, comprising 51 ncRNAs. The prognostic profile of ncRNAs was applied to an independent test set of 22 patients, correctly classifying 82% of the samples. A Kaplan-Meier analysis of the test set of patients indicated that the survival curves of high and low risk groups were significantly different (Log-rank test p = 0.0009, Hazard ratio = 23.4, 95% CI = 3.62 to 151.2) thus confirming that this classifier is useful for identifying patients at high risk of recurrence. Furthermore, these findings indicate a potential role of these intronic non-coding RNAs in the progression of prostate tumors and points to the intronic ncRNAs as potential new markers of cancer.

Non-protein coding eukaryotic genome sequences often referred to as junk DNA are estimated to encode several non-coding RNAs (ncRNAs) which may account for nearly 98% of all genomic output in humans. The output of such a wide spread transcription in eukaryotes consists of intronic, antisense and small RNAs. In addition to the classical ncRNAs such as rRNA, tRNA and small nucleolar RNAs, the eukaryotic genome encodes two distinct categories of ncRNAs, referred to as small ncRNAs and long mRNA–like ncRNAs (mlncRNAs). The long ncRNAs, which are transcribed by RNA Polymerase II, spliced and polyadenylated, are implicated in a number of regulatory processes such as imprinting, X-chromosome inactivation, DNA demethylation, transcription, RNA interference, chromatin structure dynamics and antisense mediated regulation. Expression of noncoding RNAs is altered during stress conditions and a large number of such transcripts have been identified of late. This study has identified a novel ncRNA whose expression is upregulated during viral infection of mouse brain. While we have named this RNA as VINC or virus inducible ncRNA, others have named it as NEAT1 (Hutchinson et al., 2007) and Men (Sunwoo et al., 2008). VINC/NEAT1/Men is associated with a distinct nuclear domain called paraspeckles Using a cell line as well as an animal model system we have investigated VINC in great detail and based on these studies we report that VINC is a nuclear ncRNA that localizes to paraspeckles and it interacts with the paraspeckle protein, P54nrb in both cell line model system as well as in animal tissues by a combination of in vitro and in vivo methods. We have also mapped the domains within VINC that are involved in P54nrb interactions. Till date, the only other RNA known to localise to paraspeckles is CTN-RNA. While CTN-RNA is a protein coding RNA, VINC does not code for a protein and thus VINC is the first ncRNA to be localized to paraspeckles. Further, the mechanism of nuclear retention of these two paraspeckle RNAs appears to be distinct. In case of CTN-RNA, it has been clearly shown that it is A-I edited and such hyperedited RNAs are retained by the p54/nrb mediated complex in nucleus (Zhang and Carmichael, 2001). However the mechanism by which VINC is retained in nucleus is not clear. There is apparently no A-I editing in VINC and hence VINC retention in the nucleus by binding to nuclear proteins such as p54/nrb might involve a different mechanism. It is well established of late that nuclear matrix retains RNAs and that there is a population of poly (A) RNA that is retained in nucleus (Huang et al.,1994 ; Carter et al.,1991). However the significance of such retention is not clear but it is believed that it might be important for some constitutive functions in nucleus (Nickerson et al., 1989). More investigations are needed to understand the exact functions of nuclear RNAs such as VINC in supporting the nuclear architecture. P54nrb is a multi functional nuclear protein that mediates most of its functions in association with PSF (Shav-Tal and Zipori, 2002). Phosphorylation status of P54nrb is a key determinant for its localisation to various nuclear regions. P54nrb is a multiphosphorylated protein during mitosis and its phosphorylation is mediated by PIN-1 at its C-terminus (Proteau et al., 2005). Tyrosine phosphorylation of P54nrb is essential for it to be retained in nuclear matrix (Otto et al., 2001). The N-terminal phosphorylation is speculated but not much has been investigated. The protein has two distinct RNA recognition motifs (RRMs) in its N-terminus that are responsible for its RNA binding activity. The significance of the p54/nrb-PSF heterodimer cannot be undermined as they have been shown to be important during HIV replication. The dimer is recruited by viral machinery and P54nrb has been shown to be exported to cytosol for binding to replicative complexes (Zolotukhin et al., 2003). During adenoviral replication in nucleus many SR proteins are recruited to viral replication foci and rearrangement of speckle components happen. It has been shown with respect to speckles that nuclear domains are highly dynamic and exchange of proteins depends upon the transcriptional status of cell (Lamond and Spector, 2003). Flaviviral replication complexes are hosted in nucleus and ~20% of this complex docks in nucleus and serves as an alternate site for viral replication. The presence of viral replicative complexes alters the nuclear organisation and hence modulation of gene expression is expected (Uchil et al., 2006). The up regulation of nuclear ncRNA such as VINC is definitively one of those events associated with viral replication and definitively one needs to study the various changes carefully to understand the role of VINC in virus life cycle and/or viral pathogenesis. VINC interaction with the multi-functional nuclear protein P54nrb raises interesting aspects related to function of P54nrb in JEV infection. Knockdown of P54nrb in human myeloid cell line results in abnormal size of paraspeckles and impairs chondrogenesis (Hata et al., 2008). PSF-P54nrb complex can divert many of HIV gag RNA complexes to paraspeckles thus trying to restrict viral replication. However the exact relationship between paraspeckles and its constituent proteins is not clear. The presence of ncRNA adds another new dimension to paraspeckles. It is unclear whether the ncRNA VINC is essential for paraspeckle structure but a recent study indicates that Men (VINC/NEATI) RNA may be essential for paraspeckle formation (Sunwoo et al., 2008). The exact function VINC in neuronal as well as non-neuronal cell nuclei remains elusive and more investigations are need to understand these aspects.

RNAs não codificadores longos (lncRNAs) compõem uma fração significativa do transcriptoma. Alterações na expressão de lncRNAs já foram observadas em vários cânceres humanos, mas ainda não foram exploradas no adenocarcinoma pancreático ductal (PDAC), uma doença devastadora e agressiva para a qual faltam métodos para diagnóstico precoce e tratamentos efetivos. Utilizando uma plataforma de microarranjo de cDNA com sondas para 984 lncRNAs e 2371 mRNAs, o presente estudo identificou conjuntos de lncRNAs expressos em 38 amostras clínicas pancreáticas. O enriquecimento de (i) elementos regulatórios associados às regiões promotoras (H3K4me3); (ii) possíveis inícios de transcrição (CAGE-tags); (iii) presença de elementos conservados sugere que ao menos uma fração desses RNAs seja originada a partir de unidades transcricionais independentes, reguladas e possivelmente funcionais. Foram identificadas assinaturas de expressão gênica compostas por mRNA e lncRNAs associadas ao tumor primário e à metástase pancreática. A assinatura gIenica associada à metástase apresentou enriquecimento RNAs intrônicos de loci gênicos associados à via MAPK quinase. O aumento de expressão dos transcritos intrônicos dos loci PPP3CB, MAP3K14 e DAPK1 foi confirmado por qPCR em metástases. Em conjunto, este trabalho aponta para a importância de lncRNAs intrônicos no PDAC e para a necessidade de estudos mais aprofundados para uma melhor compreensão do papel dessa classe de transcritos na biologia da doença. / Long noncoding RNAs (lncRNAs) compose a significant fraction of transcriptome. Altered expression of lncRNAs has been observed in diverse human cancers, but has not being investigated in pancreatic ductal adenocarcinoma (PDAC), a devastating and aggressive disease that lack early diagnosis methods and effective treatments. Using a cDNA microarray platform with probes interrogating 984 lncRNAs and 2371 mRNA, the present study identified subsets of lncRNAs expressed in 38 pancreatic clinical samples. Enrichment of (i) regulatory elements associated to promoter region (H3K4me3); (ii) putative transcription start site (CAGEtags) and (iii) conserved elements, suggest that at least a fraction of these RNAs could be independent transcriptional unit, regulated, an possibly functional. Gene expression signatures comprised of mRNAs and lncRNAs and associated to primary or metastatic tumors were found. A gene signature associated to metastasis was enriched in intronic ncRNAs mapping to gene loci associated to the MAPK pathway. Over expression of intronic RNAs from PPP3CB, MAP3K14 and DAPK1 was confirmed by qPCR in metastatic samples. Taken together, this study points to the importance of intronic lncRNAs in PDAC and for the need to study this class of ncRNAs in greater detail to better understand its role in the biology of PDAC.

Introdução: Os micro RNA (miRNA) são formados a partir de RNA precursores de fita dupla que contém entre 60 a 110 nucleotídeos e formam estruturas do tipo hairpin. Imediatamente após sua transcrição pela RNA polimerase II a enzima Dicer promove a clivagem do RNA precursor em seqüências menores contendo 19 a 22 nucleotídeos. Após a clivagem, o miRNA integra-se ao complexo silenciador induzido pelo RNA (RISC) que o conduz ao seu RNA mensageiro (mRNA) homólogo recém transcrito. Esta associação promove a degradação do mRNA, ou interfere na tradução da proteína caracterizando um grande mecanismo de controle da expressão dos genes. Este mecanismo está relacionado ao desenvolvimento de órgãos e tecidos, e está envolvido no processo de carcinogênese. Nosso objetivo é identificar um perfil de expressão de miRNA que defina o adenocarcinoma de próstata de prognóstico favorável e desfavorável considerando os níveis de PSA e dados anatomopatológicos. Materiais e métodos: Foram selecionados 53 pacientes com tumores desfavoráveis (mediana do escore de Gleason igual a 8, 79,2% estadiados pT3, mediana de PSA 10,1 ng/mL e mediana do volume tumoral de 23%) e 45 considerados favoráveis (mediana do escore de Gleason igual a 5, 80% estadiados pT2, mediana de PSA de 7,8 ng/mL e mediana do volume tumoral de 11,5%). O controle foi representado por 7 pacientes com hiperplasia prostática benigna (HPB). Todos os pacientes foram submetidos a prostatectomia radical pelo mesmo cirurgião. Os espécimes cirúrgicos foram examinados na sua totalidade pelo mesmo patologista. A análise dos miRNA foi feita a partir de tecido congelado e tecido incluído em parafina usando a técnica da reação em cadeia da polimerase em tempo real quantitativa (qRT-PCR) utilizando primers e sondas Taqman® específicas. O RNU43 foi usado como controle interno. Resultados: Com exceção dos miRNA 199a, 21, 15a, 16 e 25 que se mostraram subexpressos tanto nos casos desfavoráveis como nos favoráveis, houve uma diminuição global na expressão dos miRNA com redução estatisticamente significativa na expressão dos miRNA 143, 145 e 146a, 191, 218 e Let7c em tumores desfavoráveis em relação aos tumores favoráveis. Conclusão: Demonstramos que no processo de transição entre os carcinomas favoráveis e desfavoráveis de próstata existe uma perda global na expressão de miRNA que podem ser importantes controladores de expressão de uma série de genes relacionados a progressão desta neoplasia. Dados experimentais avaliando o papel desses miRNA devem ser conduzidos para que possamos definir seu papel na evolução do câncer de próstata / Introduction: micro RNA (miRNA) are formed from double-stranded RNA precursors that contain between 60-110 nucleotides and form structures such as hairpin. Immediately after their transcription by RNA polymerase II, the enzyme Dicer promotes the cleavage of precursor RNA sequences containing minor 19-22 nucleotides. After cleavage, the miRNA is part of the RNA-induced silencing complex (RISC) that leads to its messenger RNA (mRNA) newly transcribed counterpart. This association promotes the degradation of mRNA, or interferes with the protein translation characterizing a great mechanism for controlling gene expression. This mechanism is related to the development of organs and tissues, and may be involved in the process of carcinogenesis. Our goal is to identify a miRNA expression profile that distinguishes prostate adenocarcinoma of favorable and unfavorable prognosis considering the PSA and pathological findings. Material and Methods: We studied 53 patients with tumors considered unfavorable (Median of Gleason score 8, 79.2% staged pT3, median of PSA 10.1 ng/mL and median of tumor volume of 23%) and 45 considered favorable (Median of Gleason score 5, 80% staged pT2, median of PSA 7.8 ng/mL and median of tumor volume of 11.5%). The control group was represented by seven patients with benign prostatic hyperplasia (BPH). All patients underwent radical prostatectomy by the same surgeon. The surgical specimen was examined entirely by the same pathologist. The analysis of miRNA was made from frozen and paraffin embedded tissue by quantitative real-time polymerase chain reaction (qRT-PCR) using the Taqman® specific primers and probes. The RNU43 was used as a internal control. Results: Except for miRNAs 199a, 21, 15a, 16 e 25 that were underexpressed by both favorable and unfavorable prostate cancer, there was a global decrease of all miRNAs studied, and some differences were statistically significant as miRNAs 143, 145 e 146a, 191, 218 e Let7c that were underexpressed in unfavorable carcinomas compared favorable tumor. Conclusion: We have demonstrated that in the process of transition between favorable and unfavorable prostate cancer there is a global loss of expression of miRNAs. These molecules can be important controllers of a series of genes related to cancer progression. Experimental studies are needed in order to comprehend the role of these genes in prostate carcinogenesis