No description available.

The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during embryogenesis that results in the deletion of ~0.5 Gb of germline DNA from the somatic lineage. The underlying mechanism of these rearrangements remains largely unknown. miRNAs (microRNAs) and piRNAs (PIWI interacting RNAs) are two classes of small noncoding RNAs that play important roles in early vertebrate development, including differentiation of cell lineages, modulation of signaling pathways, and clearing of maternal transcripts. Here, I utilized next generation sequencing to determine the temporal expression of miRNAs, piRNAs, and other small noncoding RNAs during the first five days of lamprey embryogenesis, a time series that spans the 24-32 cell stage to the formation of the neural crest. I obtained expression patterns for thousands of miRNA and piRNA species. These studies identified several thousand small RNAs that are expressed immediately before, during, and immediately after PGR. Significant sequence variation was observed at the 3’ end of miRNAs, representing template-independent covalent modifications. Patterns observed in lamprey are consistent with expectations that the addition of adenosine and uracil residues plays a role in regulation of miRNA stability during the maternal-zygotic transition. We also identified a conserved motif present in sequences without any known annotation that is expressed exclusively during PGR. This motif is similar to binding motifs of known DNA binding and nuclear export factors, and our data could represent a novel class of small noncoding RNAs operating in lamprey.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2018-04-02T12:49:22Z No. of bitstreams: 1 GiorgioAndreBritoOliveira_DISSERT.pdf: 3458330 bytes, checksum: 434d48526b1ff4a3e12b0d1b440b6198 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2018-04-04T14:49:22Z (GMT) No. of bitstreams: 1 GiorgioAndreBritoOliveira_DISSERT.pdf: 3458330 bytes, checksum: 434d48526b1ff4a3e12b0d1b440b6198 (MD5) / Made available in DSpace on 2018-04-04T14:49:23Z (GMT). No. of bitstreams: 1 GiorgioAndreBritoOliveira_DISSERT.pdf: 3458330 bytes, checksum: 434d48526b1ff4a3e12b0d1b440b6198 (MD5) Previous issue date: 2018-02-09 / Os materiais comp?sitos s?o um novo destaque no avan?o tecnol?gico, impondo novas pesquisas relacionadas ao assunto devido a sua crescente demanda nas mais diversas ?reas. Dentre essas pesquisas surgem as que tem como objetivo facilitar as aplica??es desses materiais, atrav?s de uma r?pida apura??o das suas propriedades mec?nicas sem a necessidade de procedimentos experimentais, sendo essa fator primacial na prepara??o de projetos. Assim surgiram os modelos micromec?nicos, que ganharam destaque devido a sua praticidade, como exemplo das equa??es da Regra das Misturas e das equa??es de Halpin-Tsai. Recentemente, novos modelos computacionais vem combinando modelos micromec?nicos e aperfei?oando-os para se ter a m?xima acur?cia, como por exemplo as redes neurais artificiais (RNAs). Com base nisso, este trabalho visa a cria??o de arquiteturas de RNAs capazes de modelar o m?dulo de cisalhamento (G12) e a tens?o ?ltima de tra??o longitudinal (Xt) de comp?sitos unidirecionais. Com as RNAs treinadas e testadas, essas v?o servir como ferramentas computacionais, semelhante a fun??es, em que fornecendo as entradas teremos uma sa?da desejada. Para isso, fez-se necess?rio uma coleta de dados da literatura, que foram divididos em um conjunto de treino e um conjunto de teste, para realiza??o da valida??o cruzada. Se desenvolveram sete tipos de arquiteturas diferentes, tr?s para o G12 e quatro para o Xt, na qual essas possuem entre duas, tr?s e quatro entradas. Dentre esses modelos tr?s deles s?o considerados modelos mistos, que combina valores da sa?da da RNA com os valores obtidos vindos de modelos micromec?nicos, como o modelo de Halpin-Tsai. Ap?s o treinamento das RNAs, foi realizada uma an?lise comparativa dos valores vindos da RNA e dos valores experimentais, e ainda an?lises quantitativas e qualitativas com base no modelo de compara??o (modelo de Halpin-Tsai e modelo da Regra das Misturas), apresentando maiores valores de coeficiente de correla??o e menores valores de erro quadr?tico m?dio. / The composite materials are a new highlight in the technological advancement, consequently leading to the development of new researches due to its growing demand in the most diverse areas. Among these researches, arise those that have the objective to facilitate the application of these materials, through a fast estimation of its mechanical properties, without the need for experimental procedures, with this being the main factor in the projects preparation. Thus the micromechanical models appeared, which gained importance due to its practicality, such as the Mix Rule and the Halpin-Tsai equations. Recently, new computational models are combining micromechanical models and perfecting them to obtain maximum accuracy, as for instance in the Artifical Neural Networks application. Therefore, this work aims to create an Artificial Neural Network (ANN) architecture capable of modeling the shear modulus and ultimate longitudinal stress of unidirectional composites. When the ANN?s are trained and tested, they will serve as computational tools, similar to functions, where an input is supplied to obtain a desired output. To achieve this goal, it was necessary a collection of data in literature, which were divided in a training group and a testing group, with the cross validation between them being performed. Seven different types of architectures were developed, three for the G12 and four for the Xt, each of these with two, three and four inputs. Among these models, three of them are considered mixed models, which combines values from the output of the ANN with values obtained from the micromechanical models, such as the Halpin-Tsai. After the ANN training, a comparative analysis was performed between the values from the ANN and the experimental values, with quantitative and qualitative analysis being performed with the Halpin-Tsai model as a base for comparison, presenting higher values for the correlation coefficient and smaller values for the root mean square error.

Introdução: o transplante renal é o tratamento de escolha para uma significativa porção dos pacientes com perda crônica terminal da função renal. A rejeição aguda é uma importante complicação pós-transplante e entre outras disfunções agudas tem na biópsia do enxerto o padrão ouro para o seu diagnóstico. No entanto as biópsias apresentam uma série de limitações e riscos sendo necessário que se desenvolva biomarcadores não invasivos capazes de identificar disfunções do enxerto. Objetivos: analisar e quantificar a expressão dos microRNAs miR-142-3p, miR-155 e miR-210 em amostras de sangue periférico, urina e tecido renal coletadas de pacientes que submetidos à transplante renal que desenvolveram disfunção do enxerto. Métodos: estudo com delineamento transversal e executado no Laboratório de Biologia Molecular aplicado à Nefrologia (LABMAN), do Centro de Pesquisa Experimental do Hospital de Clínicas de Porto Alegre. As amostras são de pacientes submetidos a transplante renal que necessitaram de biópsia, por critério clínico. A expressão dos miRNAs miR-142-3p, miR-155 e miR-210 nos materiais biológicos (tecido renal, sangue periférico e células do sedimento urinário) foi avaliada através da técnica de reação em cadeia da polimerase quantitativo em tempo real. Resultados: foi encontrada, no sangue periférico uma diminuição estatisticamente significativa na expressão do miR-142-3p no grupo de pacientes com rejeição aguda (n=23) quando comparado ao grupo com outras causas de disfunção do enxerto (n=68) (P = 0,01). Não houve diferença entre os grupos na expressão do miR-155 e do miR-210, tampouco para o miR142-3p nos demais compartimentos. Conclusão: miR-142-3p mostra uma expressão diferenciada de rejeição aguda de enxertos renais, há um envolvimento deste marcador no grupo de biomarcadores moleculares em potencial para a disfunção do enxerto renal. / Background: kidney transplantation is the treatment of choice for a significant portion of patients with end-stage kidney disease. Acute rejection is a major post-transplant complication among other acute disorders and has on graft biopsy the gold standard for diagnosis. Biopsy, however it is an invasive and potentially harmful procedure so it is desirable to develop new noninvasive markers for diagnosing graft dysfunction. Objective: to analyze and quantify the expression of microRNAs miR-142-3p, miR-155 and miR-210 in the peripheral blood, urinary sediment and kidney tissue obtained from patients who developed graft dysfunction after kidney transplantation. Methods: crosssectional study performed at the Laboratory of Molecular Biology applied to Nephrology (Labman), Center of Experimental Research from Hospital de Clinicas de Porto Alegre. The samples are from kidney transplant patients who undertook indication biopsies as a part of investigation of graft dysfunction. Micro-RNAs expression was evaluated by quantitative real-time polymerase chain reaction. Results: it was found that in peripheral blood, a significant decrease in the expression of miR-142-3p occurred in patients with acute rejection (n = 23) as compared to the group of patients with other causes of graft dysfunction (n = 68), (P = 0.01). No other significant differences were found in gene expression of miR-155 and miR-210, neither for miR142-3p in the other urine or kidney tissue. Conclusion: miR-142-3p presents differential expression in the peripheral blood of patients with rejecting kidney grafts. The role of miRNAs as biomarkers for kidney graft dysfunction is worth be further explored.

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Biologia Celular, 2008. / Submitted by Diogo Trindade Fóis (diogo_fois@hotmail.com) on 2009-10-06T11:45:45Z No. of bitstreams: 1 2008_RobertoTernesArrial.pdf: 1174697 bytes, checksum: deb680a64e956cb71d50d5d028a379c8 (MD5) / Approved for entry into archive by Guimaraes Jacqueline(jacqueline.guimaraes@bce.unb.br) on 2009-11-03T17:27:16Z (GMT) No. of bitstreams: 1 2008_RobertoTernesArrial.pdf: 1174697 bytes, checksum: deb680a64e956cb71d50d5d028a379c8 (MD5) / Made available in DSpace on 2009-11-03T17:27:16Z (GMT). No. of bitstreams: 1 2008_RobertoTernesArrial.pdf: 1174697 bytes, checksum: deb680a64e956cb71d50d5d028a379c8 (MD5) Previous issue date: 2008-04 / Paracoccidioides brasiliensis (Pb) é um fungo saprófito e dimórfico de importância clínica, pois seus propágulos, quando inalados por humanos, desencadeiam a doença conhecida como paracoccidioidomicose. No ano de 2005 foi publicado o transcriptoma do Pb, apontando diversos alvos potenciais de drogas, mas ainda assim uma parte significativa dos transcritos seqüenciados não possui proteínas homólogas identificadas. Esse trabalho sugere que alguns desses RNAs possam ser não-codificadores (ncRNAs), uma classe de moléculas biologicamente funcionais que no entanto não codificam para nenhum produto protéico. Para tanto foi feita uma abordagem exclusivamente computacional, utilizando exemplos conhecidos de mRNAs e ncRNAs para treinamento de dois algoritmos de aprendizado de máquina: naive Bayes (nB) e Máquinas de Vetores de Suporte (MVS). Diversos programas descritos na literatura e desenvolvidos localmente foram usados para obter propriedades dos transcritos e de seus produtos protéicos, de forma que os algoritmos de aprendizado de máquina fossem capazes de diferenciar satisfatoriamente um mRNA de um ncRNA. O uso de várias medidas de eficiência mostra que ambos algoritmos, MVS e nB, induziram classificadores que discriminam as duas classes de RNAs de forma muito eficiente, mas também indicam que o MVS possui uma vantagem significativa em relação à sua detecção de ncRNAs. Acurácia média mensurada por validação cruzada de 10 vezes para o MVS foi de 92,4%, e para o nB, 75,3%. Quando usados no transcriptoma de Pb, o MVS e o nB detectam, respectivamente, 970 e 262 ncRNAs, dos quais a maior parte é de transcritos sem anotação e singlets, duas características que apóiam a possibilidade de que esses transcritos sejam realmente ncRNAs. Comparações a programas relacionados mostram que o programa aqui descrito apresenta um ganho em velocidade computacional sem perda de acurácia. Foi desenvolvido nesse trabalho um programa computacional de análise ab initio, designado PORTRAIT, especializado em detecção de ncRNAs em transcriptomas de organismos pouco caracterizados. __________________________________________________________________________________________ ABSTRACT / Paracoccidioides brasiliensis (Pb) is a saprophytic and dimorphic fungus of clinical importance because its propagules, when inhaled by humans, cause the disease known as paracoccidioidomycosis. In the year 2005 the Pb transcriptome was published, pointing out several potential drug targets, but still a significative amount of sequenced transcripts lack identified homologous proteins. This work suggests that these RNAs may be non-coding RNAs (ncRNAs), a class of biologically functional molecules that do not code for any protein product. Aiming this, a strictly computational approach was made, using known examples of mRNAs and ncRNAs for training two machine learning algorithms: naive Bayes (nB) and Support Vector Machines (SVM). Several programs available from literature and locally developed were used to obtain properties from transcripts and its corresponding protein products, in such a way that machine learning algorithms could successfully discriminate between mRNA and ncRNA. Several efficiency measurements show that both algorithms, SVM and nB, induced classifiers able to efficiently discriminate the two classes of RNAs, and also indicate that SVM has a significative advantage regarding ncRNA detection. Mean accuracy as estimated by 10-fold cross-validation procedure was 92.4% for SVM and 75.3% for nB. When used in the Pb transcriptome, SVM and nB detect, respectively, 970 and 262 ncRNAs, of which the majority is composed of singlets and unnanotated transcripts, two characteristics that support the possibility that these transcripts are real ncRNAs. Comparison to related works indicates that the described program offers a computational speed improvement without hindering accuracy. This work describes the design of a computational program for ab initio analysis, named PORTRAIT, specialized in detection of ncRNAs in transcriptomes from poorly characterized organisms.

Les rétrovirus endogènes sont des parasites génétiques qui s’insèrent dans l’ADN génomique. Bien que leurs insertions délétères soient éliminées par la sélection naturelle, ils prolifèrent et sont une source de plasticité génomique. L’étude de l’impact de leur mobilité sur le génome hôte est rendue difficile par le faible taux de transposition de ces éléments, réprimés par des petits ARN appelés piARNs. Nous avons développé une approche génétique permettant d’inactiver ce contrôle et de déterminer l’impact sur le génome de la drosophile, d’une transposition réplicative. Nous avons remarqué la mise en place d’autres mécanismes de répression des rétrovirus endogènes lors de la perte des piARNs pouvant ainsi limiter leur propagation. Nous avons aussi identifié de nouveaux sites d’intégrations des rétrovirus endogènes après un cycle de transposition réplicative. Cependant, le taux de transposition reste faible. Ce projet combinant différentes approches (génétique, séquençage à haut débit et bioinformatique) a permis de démontrer que la voie des piARNs n’est pas cruciale pour le maintien de l’intégrité du génome, et que d’autres mécanismes semblent intervenir afin de maintenir sa stabilité. / Endogenous retrovirsuses are genetic parasites which are inserted in the genomic DNA. Although their deleterious insertions are eliminated by natural selection, they proliferate and are a source of genomic plasticity. The study of the impact of their mobility on the host genome is made difficult by the transposition’s low rate of these elements, suppressed by a class of small RNA, called piRNA. We have developed a genetic approach to inactivate this control and determine the impact on Drosophila’s genome, after one replicative transposition. We noticed the establishment of other endogenous retroviruses repression mechanisms that are awakened after the loss of the piRNA and they are able to limit their spread. We identified new integrations sites of endogenous retrovirus after one replicative transposition. But we noticed that the transposition rate still low. This project combines different approaches (genetics, high-throughput sequencing and bioinformatics) and show the piRNA pathway is not essential to maintain genome integrity but other mechanisms involving small RNA can be implicated in the genome stability.

Exonic sequences of eukaryotic genes are interspersed with introns which when accurately removed from the primary transcript (pre-mRNA) results in a functional transcript. These splicing reactions are carried out by the spliceosome, consisting of U1, U2, U4, U5, U6 snRNAs and 150 non-snRNP proteins, which assemble onto the pre-mRNA and catalyzes the two invariant transesterification reactions (Will and Luhrmann, 2006). The flexibility in choice of splice sites allows for alternative splicing which has immensely contributed to eukaryotic genome evolution and in diversifying the metazoan proteome (Nilesen and Graveley, 2010). Dynamic yet ordered interactions between U2, U5 and U6 snRNAs and Prp8, Prp16, Prp17, Prp18, Slu7 and Prp22 splicing factors are required in vitro for second-step of splicing of budding yeast and human model transcripts (Umen and Guthrie, 1995a; Horowitz, 2012). ScSlu7 aids 3’ss selection while its strongly associated partner ScPrp18 stabilises U5 snRNA-exonic interactions (James et al., 2002; Aronova et al., 2007). These factors are dispensable in vitro, for the splicing of introns with short branch nucleotide to 3’ss distances (Brys and Schwer, 1996; Zhang and Schwer, 1997). Nearly 43% of fission yeast genes have short introns, with degenerate splice-signals and unconventional Py(n) tracts (Kuhn and Kaufer, 2003). As these features differ extensively from budding yeast and are interestingly more representative of fungal and other eukaryotic introns, fission yeast is an attractive unicellular model to investigate alternate splice-site recognition and assembly mechanisms. Mechanistic details of the second catalytic step are poorly understood in fission yeast. Strikingly, mutations in 3’ss and Py(n) tract intronic cis elements, known to block second step splicing in budding yeast, cause pre-catalytic arrest with unspliced pre-mRNA accumulation in fission yeast (Romfo and Wise, 1997). Studies in our laboratory focussed on understanding the functions for fission yeast SpPrp18 and SpSlu7 predicted to be second-step factors, revealed remarkable differences as compared to their budding yeast counterparts. Unexpectedly, SpPrp18 and SpSlu7 were found by our lab to be required before catalysis and these proteins do not directly associate with each other. Genome-wide splicing studies in a missense slu7-2 mutant indicated widespread yet intron-specific splicing functions for SpSlu7 (Banerjee et al., 2013). Crucial functions were attributed to helix-5 and conserved region loop of SpPrp18 and in vivo splicing analysis in selected cellular transcripts in a missense mutant (V194R) also revealed intron-specific functions (Thesis, N Vijaykrishna). In this study, we have advanced our understanding of SpPrp18 functions by identifying its global substrates and correlating with its intron-specific roles. Through molecular and genetic approaches, we have probed its role in splicing/spliceosome assembly. We identified intronic features within substrates that increase the propensity for the requirement of SpSlu7 for efficient splicing. Further, using findings from the genome-wide alternative splicing patterns in SpSlu7 and SpPrp18 mutants, we have attempted to understand their role in splice-site choice and thus alternative splicing. Ia. Understanding global splicing functions and spliceosomal interactions of fission yeast splicing factor SpPrp18 Since SpPrp18 is an essential gene, our lab generated the strains (prp18-5int [V194R] and WTint), where the thiamine-repressible promoter allowed conditional expression of wild-type or mutant allele integrated at the heterologous leu1 locus. Splicing efficiency of certain cellular transcripts with differing intron characteristics was assessed by semi-quantitative RT-PCR studies and the data suggested intron-specific SpPrp18 roles (in collaboration with Vijaykrishna N). This prompted us to investigate the global splicing role for SpPrp18 for which we used splicing-sensitive microarrays having custom-designed probes to distinguish unspliced pre-mRNA and spliced mRNA for every individual pombe intron. RNA from prp18-5int (V194R) and WTint cells was used in these experiments. We derived a stringent dataset of 258 introns which were statistically significant and correlated in two biological replicate RNA samples, for various probes. Hierarchical clustering of this dataset showed that the depletion of wild-type SpPrp18 triggered a range of splicing phenotypes like (A) pre-mRNA accumulation with mRNA reduction (B) pre-mRNA accumulation (C) spliced mRNA reduction and (D) unchanged pre-mRNA and mRNA levels. Statistical analysis of cis motifs that may correlate with the substrate-specific SpPrp18 splicing functions was done, but the data showed a lack of a global discriminatory primary sequence feature. However, a subtle intron-specific role for Py(n) tracts located between 5’ss and BrP was deduced for SpPrp18. This lead was validated by examining the in vivo splicing efficiency of minitranscripts with wild-type or an altered Py tract length, carried out for a SpPrp18 dependent and an independent intron. To specifically address if SpPrp18 activity was required for second-step splicing we investigated, using primer extension analyses, for lariat intron-3’exon species, an intermediate formed after step 1. We observed that even in prp18-5int dbr1∆ double mutants (where lariat molecules are not degraded) the cells accumulate only unspliced pre-mRNA and not lariat intermediates, a signature of an early arrest prior to the first transesterification reaction. Strengthening these findings, positive genetic interactions were noted between prp18-5int and ts mutants in two factors (U2AF59 and SpPrp1) involved in precatalytic spliceosome assembly and activation. On the whole, our genome-wide studies indicate intron-specific pre-catalytic functions for SpPrp18 supported by genetic interactions with early acting splicing factors involved in spliceosomal assembly and activation. Ib. Identification of intronic features that determine substrate-specific splicing functions for SpSlu7 In vitro studies with ScSlu7 and hSlu7 show their influence in 3’ss selection when BrP to 3’ss distance is greater than 7 nts and 23 nts respectively; but the global substrates are not known in either species (Brys and Schwer, 1996; Chua and Reed, 1999b). Genome-wide analysis of the splicing efficiency changes in cells with the mis-sense spslu7+ mutant (slu7-2), previously carried out in our lab, revealed a spectrum of splicing defects (Banerjee et al., 2013). To further understand the intron context-specific roles for SpSlu7, we examined intronic cis features that may correlate with SpSlu7 dependence. Statistical analyses of the affected (422 introns) and unaffected categories (90 introns) revealed that intron length, BrP to 3’ss distance and AU content are multiple discriminatory cis features that govern SpSlu7 splicing functions. To assess the contribution of these intronic features we tested whether altering these cis elements changes a transcript’s dependency (or otherwise) on SpSlu7 by RT-PCR analyses. For these studies, we generated plasmid expressed mini-genes containing the respective wild-type intron or intron with altered BrP-3’ss distances. We used nab2+ I2 as a case of an intron spliced independent of SpSlu7 and rhb1+ I1 as a representative for SpSlu7 dependent intron. Experiments testing their in vivo splicing status proved that BrP-3’ss distance is a cis feature that dictates SpSlu7 splicing functions in a context-dependent manner. The intronic AU content particularly between the 5’ss and the BrP was assessed in minigene constructs where a chimeric intron was generated by swapping the low AU containing sequences in the 5’ss to BrP stretch of cdc2+ I2 with AU rich bpb1+ I1 5’ end sequences. The results reaffirmed that low intronic AU content particularly at the 5’ end co-relates with SpSlu7 dependency. Hence, we have deduced novel intronic elements, which perhaps in combination, create a contextual dependence for SpSlu7 to facilitate efficient splicing. II. Alternative splice-site selection in fission yeast and studies on the role of splicing factors SpSlu7 and SpPrp18 Budding yeast second-step splicing factors ScSlu7 and ScPrp18 mediate 3’ss choice in the single intron containing transcripts. Fission yeast genome encodes cis and trans factors that promote alternative splicing similar to higher eukaryotes. In this study, we have devised a data analysis pipeline to identify alternative splice events in multi-intronic transcripts of fission yeast. Further, we utilised this information to interrogate the global role for SpSlu7 and SpPrp18 in alternate splice site selection. We mapped the microarray probe sequences corresponding to all theoretically possible non-consecutive splice junctions of S. pombe transcripts onto two independent experimental next-generation (NGS) transcriptomes from wild-type samples and identified 104 exon skipping events with NGS reads more than 3 (Wilhelm et al., 2008; Rhind et al., 2011). We further generated a stringent list of ten exon skipping events having high sequence reads as well as raw intensity value in our microarray experiments with wild-type cells. Two representative events from this list, an abundant rps13+ exon 2 skipped alternative mRNA and less abundant ats1+ exon 3 skipped alternative mRNA were then taken up for experimental analyses by semi-quantitative RT-PCR assays. We confirmed these events and further noted that SpSlu7 and SpPrp18 were required for the constitutive splicing of ats1+ E2-I2-E3-I3-E4 cassette. On the other hand, SpSlu7, and not SpPrp18, exerted a subtle influence on the skipping of exon 3. In addition to exon 3 skipped mRNA, we detected an intron 3 retained ats1+ alternative mRNA (E2-E3-I3-E4) in wild-type cells. Assessment of this event in cells metabolically depleted of SpSlu7 and SpPrp18 showed a reduced abundance of this species in both instances. This suggests a role for functional SpSlu7 and SpPrp18 in retaining intron 3 in ats1+ transcripts in vivo. Among the ten microarray probes, custom-designed to detect specifically the mRNA isoforms arising from altered use of donor 5’ splice sites, we were able to detect in wild-type cells the utilisation of a downstream alternate 5’ss in intron 1 of D-Tyr-tRNA deacylase. Comparative assessment of this splicing event in prp18-5int and slu7-2 mutant cells revealed that SpPrp18 is preferentially required for the utilisation of its alternative 5’ss and such a role has not yet been attributed to its budding yeast and human homologs. On the other hand, SpSlu7 was required equally for utilisation of canonical and non-canonical 5’ss. Differential requirement for SpSlu7 for the utilisation of an upstream non-canonical 3’ss and the canonical 3’ss in DUF3074 intron 1, was noted. This role of SpSlu7 in 3’ss selection is similar to that known from in vitro studies of its budding yeast and human counterparts. Overall, we identified and experimentally validated novel alternate splice events in fission yeast and we infer an important role for SpSlu7 and SpPrp18 in both 5’ss and 3’ss selection.

RNA silencing is a cellular mechanism of post-transcriptional gene regulation which is highly conserved among the plant and animal kingdoms of life, and plays a critical part of developmental biology, maintenance of homeostasis, and host-pathogen interactions. The pathway is engaged by small double-stranded (ds)RNA molecules (small RNAs), which effect sequence specific gene silencing by targeting complementary RNA sequences. There are several classes of small RNAs which engage the pathway. MicroRNAs (miRNAs) are expressed in the genome as endogenous regulators of gene expression. Short-interfering RNAs (siRNAs) are usually from exogenous sources such as viral-derived short-interfering RNAs, or synthetic siRNAs which are applied to cells or organisms to inhibit expression of specific genes. The p19 protein is a viral suppressor of RNA silencing (VSRS) endogenous to tombusviruses, which binds small RNA duplexes of any sequence with extremely high affinity. Because of its unique binding properties, recombinant p19 proteins are an excellent platform for tool development surrounding the RNA silencing pathway and are used extensively in novel applications for modulating the activity of small RNAs in living systems and for detecting small RNAs in biological samples. Herein we present work that has increased the breadth of p19’s utility as a biotechnology tool in three distinct realms. First, we present a chemical biology approach which combines p19 and small molecules for potent inhibition of the RNA silencing pathway in human cells. Secondly, we present the development of a novel fusion protein between p19 and a cell penetrating peptide (CPP), which functions as an siRNA delivery agent to allow gene knockdown in human cells. Thirdly, we have improved the utility of p19 for detecting and sequestering human miRNAs through rationally designing the binding surface; we describe mutations which dramatically enhance p19's affinity for human miRNA-122. The work presented here adds to the growing repertoire of engineered RNA binding proteins (RBPs) as tools for studying small RNA molecules and modulating their activity for applications in human therapeutics.

Introdução: o transplante renal é o tratamento de escolha para uma significativa porção dos pacientes com perda crônica terminal da função renal. A rejeição aguda é uma importante complicação pós-transplante e entre outras disfunções agudas tem na biópsia do enxerto o padrão ouro para o seu diagnóstico. No entanto as biópsias apresentam uma série de limitações e riscos sendo necessário que se desenvolva biomarcadores não invasivos capazes de identificar disfunções do enxerto. Objetivos: analisar e quantificar a expressão dos microRNAs miR-142-3p, miR-155 e miR-210 em amostras de sangue periférico, urina e tecido renal coletadas de pacientes que submetidos à transplante renal que desenvolveram disfunção do enxerto. Métodos: estudo com delineamento transversal e executado no Laboratório de Biologia Molecular aplicado à Nefrologia (LABMAN), do Centro de Pesquisa Experimental do Hospital de Clínicas de Porto Alegre. As amostras são de pacientes submetidos a transplante renal que necessitaram de biópsia, por critério clínico. A expressão dos miRNAs miR-142-3p, miR-155 e miR-210 nos materiais biológicos (tecido renal, sangue periférico e células do sedimento urinário) foi avaliada através da técnica de reação em cadeia da polimerase quantitativo em tempo real. Resultados: foi encontrada, no sangue periférico uma diminuição estatisticamente significativa na expressão do miR-142-3p no grupo de pacientes com rejeição aguda (n=23) quando comparado ao grupo com outras causas de disfunção do enxerto (n=68) (P = 0,01). Não houve diferença entre os grupos na expressão do miR-155 e do miR-210, tampouco para o miR142-3p nos demais compartimentos. Conclusão: miR-142-3p mostra uma expressão diferenciada de rejeição aguda de enxertos renais, há um envolvimento deste marcador no grupo de biomarcadores moleculares em potencial para a disfunção do enxerto renal. / Background: kidney transplantation is the treatment of choice for a significant portion of patients with end-stage kidney disease. Acute rejection is a major post-transplant complication among other acute disorders and has on graft biopsy the gold standard for diagnosis. Biopsy, however it is an invasive and potentially harmful procedure so it is desirable to develop new noninvasive markers for diagnosing graft dysfunction. Objective: to analyze and quantify the expression of microRNAs miR-142-3p, miR-155 and miR-210 in the peripheral blood, urinary sediment and kidney tissue obtained from patients who developed graft dysfunction after kidney transplantation. Methods: crosssectional study performed at the Laboratory of Molecular Biology applied to Nephrology (Labman), Center of Experimental Research from Hospital de Clinicas de Porto Alegre. The samples are from kidney transplant patients who undertook indication biopsies as a part of investigation of graft dysfunction. Micro-RNAs expression was evaluated by quantitative real-time polymerase chain reaction. Results: it was found that in peripheral blood, a significant decrease in the expression of miR-142-3p occurred in patients with acute rejection (n = 23) as compared to the group of patients with other causes of graft dysfunction (n = 68), (P = 0.01). No other significant differences were found in gene expression of miR-155 and miR-210, neither for miR142-3p in the other urine or kidney tissue. Conclusion: miR-142-3p presents differential expression in the peripheral blood of patients with rejecting kidney grafts. The role of miRNAs as biomarkers for kidney graft dysfunction is worth be further explored.

La récente découverte de nouvelles classes de petits ARN a ouvert la voie permettant l’exploration de nouvelles régulations des évènements physiopathologiques. Nous avons récemment démontré que les petits ARN dérivés des RNY (s-RNY) forment une classe indépendante de biomarqueurs permettant la détection de lésions coronariennes et sont associés au fardeau athérosclérotique. Ici, nous étudions le rôle des s-RNY dans les monocytes/macrophages humains et murins et avons démontré que dans les monocytes/macrophages chargées en graisse l’expression des s-RNY est corrélée dans le temps avec l’activation de la mort cellulaire dirigée par les caspases et de l’inflammation via la voie NF-κB. Des expériences de gain ou de perte de fonction ont démontré que l’expression même des s-RNY active la caspase 3 et l’activation de NF-κB. Etant donné que, dans les maladies cardiovasculaires, les s-RNY sont associés à Ro60 et circulent dans le sang de patients, nous avons étudié la fonction extracellulaire du complexe Ro60/s-RNY. Nos données démontrent que ce complexe induit la mort cellulaire ainsi que l’inflammation, lorsqu’il est ajouté au milieu de culture de monocytes/macrophages. Enfin, nous démontrons aussi que la fonction des s-RNY se fait par l’intermédiaire du récepteur de type Toll, TLR7. En utilisant un inhibiteur spécifique des TLR7, nous avons bloqué les effets intracellulaires aussi bien que les effets extracellulaires des s-RNY. Ces résultats positionnent les s-RNY en tant que molécules significatives qui vont impacter la physiopathologie des macrophages, indiquant leur rôle potentiel en tant que médiateur des maladies inflammatoires comme l’athérosclérose / The recent discovery of new classes of small RNAs has opened unknown territories to explore new regulations of physiopathological events. We have recently demonstrated that RNY-derived small RNAs (referred to as s-RNYs) are an independent class of clinical biomarkers to detect coronary artery lesions and are associated to atherosclerosis burden. Here, we have studied the role of s-RNYs in human and mouse monocytes/macrophages and have shown that in lipid-laden monocytes/macrophages s-RNY expression is timely correlated to the activation of both NF-κB and caspase 3-dependent cell death pathways. Loss- or gain-of- function experiments demonstrated that s-RNYs activate caspase 3 and NF-κB signaling pathways ultimately promoting cell death and inflammatory responses. Since, in atherosclerosis, Ro60-associated s-RNYs generated by apoptotic macrophages are released in the blood of patients, we have investigated the extracellular function of the s-RNY/Ro60 complex. Our data demonstrated that s-RNY/Ro60 complex induces caspase 3-dependent cell death and NF-κB-dependent inflammation, when added to the medium of cultured monocytes/macrophages. Finally, we have shown that s-RNY function is mediated by Toll-like receptor 7 (TLR7). Indeed using chloroquine, which disrupts signaling of endosome-localized Toll-like receptors (TLRs) or a more specific TLR7 antagonist, we blocked the effect of either intracellular or extracellular s-RNYs. These results position s-RNYs as relevant novel functional molecules that impacts on macrophage physiopathology, indicating their potential role as mediators of inflammatory diseases, such as atherosclerosis