The serine/arginine-rich (SR-) family proteins constitute a diverse group of pre-mRNA splicing factors that are essential for viability. They can be characterised based on the presence of one or two RRMs and an RS domain. A subset, of which SRSF1 is the prototype, is capable of nucleocytoplasmic shuttling; a process governed by continual cyclic phosphorylation of the RS domain. In contrast, SRSF2, another member of the SR family, is unable to shuttle due to the presence of a nuclear retention sequence (NRS) at the C-terminus of its RS domain. When this NRS is fused to SRSF1, it prevents nucleocytoplasmic shuttling of the SRSF1-NRS fusion protein. In addition to its nuclear roles, SRSF1 is directly associated with the translation machinery and can activate mRNA translation of target transcripts via an mTOR-dependent mechanism. The specific mRNA translational targets that SRSF1 serves to regulate encode numerous factors including RNA processing factors and cell-cycle proteins. The aim of this work is to study the physiological relevance of SRSF1 cytoplasmic functions, as previous data have relied on overexpression systems. CRISPR/Cas9 editing was used to knock-in the NRS naturally present in SRSF2 at the SRSF1 genomic locus, creating an SRSF1-NRS fusion protein. After numerous attempts, it was only possible to obtain a single viable homozygous clone in mouse embryonic stem cells (mESCs), despite being able to successfully tag the genomic SRSF1 locus. This strongly suggests that the ablation of SRSF1 shuttling ability is highly selected against in mESCs. To assess the physiological importance of SRSF1 nucleocytoplasmic shuttling during development, a mouse model for SRSF1-NRS was also developed. SRSF1-NRS homozygous mice are born at correct Mendelian ratios, but are small in size and present with severe hydrocephalus. Finally, proteomics was used to identify interactors of endogenous cytoplasmic SRSF1 and those that bind the NRS of SRSF2 to gain insights into the mechanism of nuclear retention for non-shuttling SR proteins. In summary, this work analyses the physiological relevance of cytoplasmic SRSF1 function and the consequences of the SRSF1-NRS allele in mouse development.

Egg activation is a series of highly coordinated processes that prepare the mature oocyte for embryogenesis. Typically associated with fertilisation, egg activation results in the resumption of the cell cycle, expression of maternal mRNAs and cross-linking of the vitelline membrane. While some aspects of egg activation, such as initiation factors in mammals and environmental cues in sea animals, have been well-documented, the mechanics of egg activation in many animals are still not well understood. This is especially true for animals where fertilisation and egg activation are unlinked. In order to elucidate how egg activation is regulated independently of fertilisation, I use Drosophila melanogaster as a model system. This insect provides extensive genetic tools, ease of manipulation for experimentation and is amenable for imaging. Through visualisation of calcium, Processing bodies and meiotic spindles, I show that osmotic pressure acts as an initiation cue for the calcium wave and downstream processes, including the resumption of cell cycle and the dispersion of the translational repression sites. I further show that aquaporin channels, together with external sodium ions, play a role in coordinating swelling of the oocyte in response to the osmotic pressure. I proceed to identify the requirement of internal calcium sources together with a dynamic actin cytoskeleton for a calcium wave to occur. Through co-visualisation of calcium and actin, I provide the first evidence that the calcium wave is followed by a wavefront of non-cortical F-actin at egg activation, which requires the calcium wave. Genetic analysis supports a model where changes in osmotic pressure trigger the calcium wave via stretch sensitive calcium channels in the oocyte membrane and the calcium wave is relayed by nearby channels via the actin cytoskeleton. My work concludes that the mechanism of egg activation in Drosophila is more similar to plants, compared to most vertebrates.

O VEGF é um fator mitogênico específico de células endoteliais que promove diferenciação celular materno-fetal placentária quando ligado a seus receptores (Flt-1 e KDR). Sua expressão é controlada por mecanismos autócrinos e parácrinos e está associada ao desenvolvimento da placenta. A placenta bovina foi utilizada como modelo de estudo por apresentar a facilidade de se avaliar os componentes do sistema VEGF em diferentes fases gestacionais. Como objetivo este estudo buscou analisar o fator de crescimento vascular endotelial (VEGF) e seus receptores através da técnica de PCR em tempo real no início, meio e fim de gestação. Para tanto, amostras de placentomas, região interplacentomal e corpo lúteo foram coletadas em diferentes fases gestacionais. Foram utilizados placentomas de animais clonados obtidos apenas aos 270 dias de gestação e estas amostras foram comparadas aos animais não clonados na mesma fase. A expressão do VEGF no placentoma apresentou um decréscimo (p < 0.05) no final da gestação (270 dias) em relação à expressão do VEGF aos 90 dias. A expressão do Flt-1 e do KDR na região interplacentomal foi semelhante desde os 45 até 90 dias de gestação e apresentou um aumento significativo (p < 0.05) aos 150 dias. No corpo lúteo gestacional, a expressão do VEGF aos 210 dias foi maior (p ≤ 0.05) em relação a 90 e 150 dias; observou-se também baixa expressão do KDR aos 90 dias de gestação (p < 0.05) em relação aos 210 dias. Pode-se concluir que a regulação da expressão do VEGF variou em relação aos seus receptores nos três tecidos avaliados. Placentomas de bovinos clonados não apresentaram diferenças significativas em relação à expressão do sistema VEGF se comparados aos placentomas de animais não clonados sugerindo ser esta expressão equivalente em placentas de animais clonados que vieram a termo. / The VEGF is a specific endothelial mitogenic factor that promotes feto-maternal cell differentiation in placenta through binding to its receptors (Flt-1 and KDR). Their expression is controlled by autocrine and paracrine mechanisms that are associated to placenta development. The bovine placenta was used in this study as a model due to easiness of evaluation of VEGF system components in different phases of pregnancy. The objective of this study was to analyze the vascular endothelial growth factor (VEGF) and its receptors expression using the real time PCR technique in the beginning, half and end of pregnancy. Furthermore, placentome samples, interplacentomal areas and corpus luteum were collected in different gestational phases for comparative studies. Placentome of cloned animals were analyzed at 270 days of pregnancy and compared to non-cloned animals in the same phase. The expression of VEGF in the placentome presented a decrease of expression (p < 0.05) in the end of the gestation (270 days) in relation to 90 days. The expression of Flt-1 and of KDR in interplacentomal area was similar from 45 to 90 days of pregnancy with a significant increase (p <0.05) observed at 150 days. In the gestational corpus luteum, the expression of VEGF at 210 days was higher (p ≤ 0.05) in comparison to 90 and 150 days. In the same tissue KDR expression at 90 days was lower (p < 0.05) in relation to 210 days. In conclusion the regulation VEGF varied in relation to its receptors expression in all three studied tissues. Cloned placentomes showed no significant differences in VEGF system expression compared to the placentome of non-cloned animals, suggesting there is an equivalent expression in placentas from cloned animals that came to term.

Le fer est un élément essentiel pour les cellules car il est le cofacteur de nombreuses protéines impliquées dans de multiples processus biologiques comme la photosynthèse et la respiration. Cependant, l'excès de fer peut être délétère pour la cellule, car il peut réagir avec l'oxygène pour former des espèces réactives de l'oxygène (ROS). Les ferritines sont des protéines chloroplastiques codées par le génome nucléaire permettant de stocker le fer en excès sous forme non toxique. Chez les végétaux, la synthèse des ferritines est majoritairement régulée au niveau transcriptionnel en réponse au fer contrairement aux animaux où elle est majoritairement régulée au niveau post-transcriptionnel. Toutefois, une régulation post-transcriptionnelle a été mise en évidence pour le gène de ferritine AtFer1. L'ARNm d'AtFer1 est déstabilisé en réponse à un stress oxydatif généré par un excès de fer. Cette régulation fait intervenir un élément cis nommé DST (DownSTream) localisé dans la région 3' transcrite non traduite de ce transcrit (3'UTR). Chez deux mutants précédemment identifiés comme agissant en trans (dst1 et dst2), cette régulation est affectée. Une caractérisation physiologique de ces mutants a permis de montrer que cette voie de dégradation est un mécanisme essentiel contrôlant la physiologie et la croissance de la plante en réponse à un stress oxydatif. D'autre part, l'expression d'AtFer1 ainsi que d'autres gènes codant des protéines chloroplastiques est régulée par un acteur de la machinerie de dégradation des ARNm, l'exoribonucléase XRN4. Ces ARNm codant des protéines chloroplastiques seraient localisés à la surface des chloroplastes. Cette localisation ferait intervenir des acteurs de la machinerie de dégradation des ARNm. La localisation subcellulaire du transcrit AtFer1 a été estimée par deux approches. L'ARNm d'AtFer1 a été visualisé par une technique d'imagerie, l'hybridation in situ révélé par fluorescence (FISH) (i). L'accumulation d'ARNm codant des protéines chloroplastiques a été évaluée dans deux fractions (chloroplastes isolés et feuilles entière) afin de savoir si certain ARNm se retrouvent enrichis dans la fraction chloroplastique (ii). Les résultats obtenus suggèrent que l'ARNm d'AtFer1 serait localisé autour des chloroplastes, cependant cette localisation ne semble pas être affectée chez le mutant xrn4. Enfin, ce travail a permis de caractériser la régulation et la fonction des ferritines dans les racines d'Arabidopsis. Le fer en excès induit la synthèse de ferritines dans les racines, AtFer1 puis AtFer3 sont les gènes de ferritines les plus exprimés dans cet organe. Les racines de plantes cultivées en excès de fer présentent des spots de fer dans les cellules de l'endoderme et du péricycle, là où l'expression des gènes AtFer1 et AtFer3 est retrouvée. Ces spots sont absents dans un triple mutant fer1-3-4. L'excès de fer diminue la longueur de la racine primaire de manière indépendante des ferritines. Par contre, l'excès de fer modifie la densité et l'élongation des racines latérales, ces deux modifications requièrent la présence des ferritines. Lors d'un excès de fer, les ferritines participent à la mise en place du gradient de H2O2 et de O2.- entre les zones de prolifération et de différentiations. Ce gradient est impliqué dans le contrôle la croissance racinaire. / Iron is essential for cells because it is the cofactor of many proteins involved in many biological processes such as photosynthesis and respiration. However, iron in excess can be deleterious to the cell due to its capacity to react with oxygen to form reactive oxygen species (ROS). Ferritins are plastidial proteins encoded by nuclear genes in order to store iron in a safe form. In plants, ferritin synthesis is mainly regulated at the transcriptional level in response to iron in contrast to animals, where it is mainly regulated at the post-transcriptional level.However, post-transcriptional regulation has been shown for the ferritin gene AtFer1. The AtFer1 mRNA is destabilized in response to oxidative stress generated by an excess of iron. This regulation involves a cis element called DST (DownSTream) located in the 3' untranslated region (3'-UTR) of this transcript. In two mutants previously identified as trans-acting (dst1 and dst2), this regulation is affected. Physiological characterizations of these mutants have shown this pathway is an important mechanism to control physiology and plant growth in response to oxidative stress.On the other hand, AtFer1 expression and expression of other genes encoding chloroplast proteins are regulated by a component of the mRNA decay machinery, the exoribonuclease XRN4. These mRNAs encoding chloroplast proteins would be localized on the surface of chloroplasts. This location would involve component of the mRNA decay machinery. The subcellular localization of AtFer1 mRNA was estimated by two approaches. AtFer1 mRNA was visualized by an imaging technique, fluorescent in situ hybridization revealed by (FISH) (i). Accumulation of mRNA encoding chloroplast proteins was evaluated in two fractions (purified chloroplasts and total leaves) to determine if some mRNAs are found enriched in the chloroplast fraction (ii) . Our results suggest that the AtFer1 mRNA is localized around chloroplasts, however, this location does not seem to be affected in the xrn4 mutant. Finally, this work has shown the regulation and function of ferritins in the roots of Arabidopsis. Iron in excess induces ferritin synthesis in roots, and AtFer1 then AtFer3 are the most expressed ferritin genes in this organ. Roots grown in iron excess present spots of iron in the cellular layers of the endoderm and pericycle, where AtFer1 and AtFer3 ferritin genes are expressed. This staining disappears in a triple fer1-3-4 ferritin mutant. Fe in excess decreases primary root length independently of the ferritins. In contrast, Fe excess mediated alteration of lateral root density and mean length requires ferritins, in particular at the highest Fe concentration tested. During an iron excess, ferritin are involved in the establishment of the H2O2 and O2.- gradient between proliferation and differentiation zones. This gradient is known to control of root growth.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Este trabalho tem como objetivo avaliar a estabilidade de genes de referÃncia e a expressÃo das proteÃnas morfogenÃticas Ãsseas (BMP-2, 4, 6, 7 e 15), seus receptores (BMPR-IA, IB e II) e seus mensageiros intracelulares (SMADs-1, 5 e 8) em folÃculos caprinos antes e apÃs cultivo por 18 dias. Para avaliar a estabilidade dos genes de referÃncia e o nÃvel de expressÃo das BMPs, receptores e SMADs, folÃculos com aproximadamente 0,2, 0,5 e 1 mm foram isolados mecanicamente de ovÃrios caprinos. AlÃm disso, folÃculos com aproximadamente 0,2 mm foram isolados e cultivados por 18 dias em meio de cultura suplementado com FSH. ApÃs a extraÃÃo do RNA total e sÃntese de cDNA, foi realizada a quantificaÃÃo do RNAm, por PCR em tempo real, utilizando-se primers especÃficos para genes de referÃncia (β-actina, PGK, GAPDH, β-tubulina, UBQ, RPL-19, rRNA18S), e para as BMPs (2, 4, 6, 7 e 15) receptores de BMPs (BMPR-IA, IB e II) e SMADs (1, 5 e 8). Os resultados mostraram que β-tubulina e PGK sÃo os genes de referÃncia mais estÃveis em folÃculos frescos prÃ-antrais e antrais caprinos. Os RNAs mensageiros para as BMPs (2, 4, 6, 7 e 15), seus receptores (BMPR-IA, IB e II) e SMADs (1, 5 e 8) sÃo expressos em diferentes nÃveis em folÃculos prÃ-antrais e antrais caprinos, sendo que a expressÃo do RNAm para BMP-4, BMP-6 e BMP-7 em folÃculos de 1 mm sÃo significativamente maiores do que em folÃculos de 0,2 e 0,5 mm. Entretanto, os nÃveis de RNAm para BMP-2 foi reduzido em folÃculos de 1 mm, jà os nÃveis de BMP-15 nÃo diferiram entre as categorias foliculares analisadas. Os nÃveis de RNAm para BMPR-IB foram maiores em folÃculos de 0,2 mm do que em folÃculos de 0,5 e 1 mm, enquanto que o RNAm para BMPR-II foi significativamente maior em folÃculos de 0,5 mm do que em folÃculos de 0,2 e 1 mm. Por outro lado, nÃveis de RNAm para BMPR-1A nÃo diferiram entre folÃculos analisados. Os nÃveis de RNAm para SMAD-5 foram significativamente maiores em folÃculos de 0,2 mm do que em folÃculos de 0,5 e 1 mm. Contudo, folÃculos de 0,5 mm mostraram nÃveis maiores de RNAm para SMAD-8 do que folÃculos de 0,2 e 1 mm. Os nÃveis de RNAm para SMAD-1 nÃo diferiram entre os folÃculos. ApÃs as comparaÃÃes dentro de cada categoria folÃcular, BMP-15 foi mais expressa do que BMP-7 em folÃculos de 0,2 e 0,5 mm. Em folÃculos de 0,5 mm a expressÃo do BMPR-IB foi maior do que BMPR-II. Em todas as trÃs categorias foliculares estudadas, a expressÃo da SMAD-5 foi superior a SMAD-8. ApÃs o cultivo, os folÃculos apresentaram reduÃÃo dos nÃveis de RNAm para BMP-2, BMP-4, BMP-7, BMPR-IA e SMAD-5. Em conclusÃo, β-tubulina e PGK sÃo os dois genes housekeeping mais estÃveis para folÃculos frescos caprinos com 0,2, 0,5 e 1 mm de diÃmetro. BMPs, seus receptores e SMADs apresentam padrÃes de expressÃo especÃficos em cada categoria folicular estudada. No entanto, em folÃculos cultivados hà uma variaÃÃo na expressÃo dos componentes do sistema BMP, diferindo da expressÃo in vivo de folÃculos com o mesmo tamanho. / The aims this study to evaluate the stability of reference genes and the expression of bone morphogenetic protein (BMP-2, 4, 6, 7 and 15), their receptors (BMPR-IA, IB and II) and intracellular messengers (SMADs- 1, 5 and 8) in goat follicles before and after culture for 18 days. To evaluate the stability of reference genes and the expression of BMPs, receptors and SMADs, follicles of approximately 0.2, 0.5 and 1 mm were mechanically isolated from goats ovaries. In addition, approximately 0.2 mm follicles were isolated and cultured for 18 days in culture medium supplemented with FSH. Both fresh and cultured follicles were subjected to total RNA extraction and synthesis of cDNA, the quantification of mRNA was carried out by real-time PCR using specific primers for genes of reference (GAPDH, β-tubulin, β-actin, PGK, UBQ, RPL - 19, rRNA18S) and BMPs (2, 4, 6, 7 and 15) receptors of BMPs (BMPR-IA, IB and II) and SMADs (1, 5 and 8). Results showed that β-tubulin and PGK are the most stable reference genes in goats preantral and antral follicles. The messengers RNA for BMP (2, 4, 6, 7 and 15), their receptors (BMPR-IA, IB and II) and Smads (1, 5 and 8) are expressed at different levels in preantral and antral goats, and mRNA expression for BMP-4, BMP-6 and BMP-7 in 1-mm follicles are significantly higher than in follicles of 0.2 and 0.5 mm. However, the levels of mRNA for BMP-2 were reduced in follicles 1 mm, as BMP-15 did not differ between follicular categories. The levels of mRNA for BMPR-IB were higher in follicles of 0.2 mm than in follicles of 0.5 and 1 mm, whereas the mRNA for BMPR-II was significantly higher in follicles than 0.5 mm in follicles of 0.2 to 1 mm. Moreover, mRNA levels for BMPR-1A did not differ between follicles examined. The levels of mRNA for SMAD-5 were significantly higher in 0.2 mm follicles than in follicles of 0.5 and 1 mm. However, follicles of 0.5 mm showed higher levels of mRNA for SMAD-8 than follicles 0.2 and 1 mm. The levels of mRNA for SMAD-1 did not differ between follicles. After the comparisons within each category follicle, BMP-15 expression was higher than BMP-7 in follicles between 0.2 and 0.5 mm. Follicles 0.5 mm in the expression of BMPR-IB was greater than BMPR-II. In all three follicular categories studied, the expression of SMAD-5 was superior to SMAD-8. After culture, follicles showed reduced levels of mRNA for BMP-2, BMP-4, BMP-7, BMPR-IA and SMAD-5. In conclusion, β-tubulin and PGK genes are the two most stable housekeeping for fresh goat follicles 0.2, 0.5 to 1 mm in diameter. BMPs, their receptors and SMADs have specific expression patterns in each category follicular studied. However, in cultured follicles showed a variation in the variation in the expression of BMP system components, differing from in vivo expression of follicles with the same size.

Osteosarcoma is the most common primary malignancy of bone. 5-year survival has remained stable at around 60-70% for 40 years. However, a number of patients will suffer from recurrent and/or metastatic disease representing a large unmet clinical need. CSPG4 is a transmembrane protein which is expressed on a number of progenitor cells and tumour types. Preliminary work had found CSPG4 present in osteosarcoma tumour samples. In this study, CSPG4 mRNA and protein expression was demonstrated in clinical samples and model cell lines. CSPG4 mRNA is overexpressed in osteosarcoma samples compared to mature osteoblast cells, the putative cell of origin for osteosarcoma. In a cohort of patients, CSPG4 protein expression was found on 86% of samples. Furthermore, CSPG4 expression was demonstrated in U2OS, MG63, HOS, HOS-MNNG and 143B osteosarcoma cell lines. CSPG4 protein expression was successfully deleted in 143B cells using CRISPR/Cas9 technology. Two stable CSPG4-negative cell lines were produced. CSPG4 expression was then reintroduced into negative cell lines, as well as the parental 143B cell line. This created a panel of 6 cell lines with differing CSPG4 expression. Furthermore, siRNA treatment of U2OS, MG63, 143B and U87MG cell lines reduced CSPG4 expression. These cells provided another panel with varying CSPG4 expression for in vitro investigation. In vitro experiments failed to demonstrate a role for CSPG4 in osteosarcoma tumorigenesis. The CRISPR/Cas9 cell panel found that CSPG4 expression did not influence cell proliferation, adhesion and spreading on fibronectin or collagen-I, cell migration, chemosensitivity or anchorage-independent growth. Similarly, the siRNA cell panel found that CSPG4 expression did not influence cell proliferation or anchorage-independent growth. In vivo experimentation did not demonstrate a role for CSPG4 in mediating osteosarcoma tumour growth or metastatic spread. Treatment with a sc-Fv antibody fragment failed to demonstrate specific toxicity of CSPG4-positive cell lines. These results indicate that CSPG4 plays no role in osteosarcoma tumour cell behaviour. However, due to its wide expression pattern it represents a viable therapeutic option for drug targeting.

C-MYC is a transcription factor and a potent driver of many human cancers. In addition to regulating transcription, C-MYC promotes formation of the mRNA cap which is important for transcript maturation and translation. However, the mechanistic details of C-MYC-dependent mRNA capping are not fully understood. Since anti-cancer strategies to directly target the C-MYC protein have had limited success, enzymatic co-factors or effectors of C-MYC present attractive alternatives for therapeutic intervention of C-MYC-driven cancers. mRNA capping enzyme (CE) initiates mRNA cap formation by catalysing the linkage of inverted guanosine via a triphosphate bridge to the first transcribed nucleotide. The involvement of CE in C-MYC-dependent mRNA capping and C-MYC function has not yet been explored. Therefore, I sought to determine whether C-MYC regulates CE, and whether CE is required for C-MYC function. I found that C-MYC promotes CE recruitment to RNA polymerase II (RNA pol II) transcription complexes and to regions proximal to transcription start sites on chromatin. Consistently, C-MYC increases RNA pol II-associated CE activity. Interestingly, cells driven by C-MYC are highly dependent on CE for C-MYC-induced target gene expression and cell transformation, but only when C-MYC is overexpressed; C-MYC-independent cells or cells retaining normal control of C-MYC expression are insensitive to CE inhibition. C-MYC expression is also dependent on CE. Taken together, I present a bidirectional regulatory relationship between C-MYC and CE which is potentially therapeutically relevant. Studies here strongly suggest that inhibiting CE is an attractive strategy to selectively target cancer cells which have acquired deregulated C-MYC.

Nonsense-mediated mRNA decay (NMD) is an important protective mechanism to guard against erroneous transcripts particularly mRNA transcripts containing premature termination codons (PTC). In classical teaching, such erroneous transcripts (called nonsense-mediated decay targeted RNA, nt-RNA here) are considered as incidental non-specific side-products of the cellular transcription machinery and they are rapidly cleared by NMD and thus they exists in scanty quantity inside a cell (i.e. at a very low steady state abundance). As a side product of stochastic transcriptional error, they are also commonly considered to carry no biologic function. / By analysis of a large collection of RNA-seq data in TCGA (over 4000 samples and the hard disk storage was over 50 TB), it was found that nt-RNA were produced in large amount for some genes, sometimes, they were even more abundant than the normal transcripts of the corresponding genes. / Based on the hypothesis that some nt-RNA are specifically produced by a biological process (in contrast to a process happened by chance), the aims of this work are: 1) To quantify the expression of nt-RNA (survey of the spectrum); 2) To examine the relationship between nt-RNA and protein expression (biological roles); 3) To detect nt-RNAs that affect prognosis of cancer (biological roles); 4) To apply nt-RNA as diagnostic biomarkers for cancer (application); 5) To identify nt-RNAs to classify tumors for unknown primary (CUP, application). / Firstly, nt-RNA were defined from Gene databases and all PTC containing transcripts were compared to their corresponding normal transcripts to locate specific signature tags (both short segments of sequences and splice junctions) for each of the nt-RNA. And the presence and counts of these nt-RNA signature tag were searched in all RNA reads of RNA-seq datasets. Such search and counting produced the read counts of each nt-RNA signature tag and all RNA-read containing such tags are targets for NMD. RNA-seq datasets used in this study included TCGA normal samples, TCGA tumor samples and cancer cell lines for 13 cancer types. / In the example of KIRC, it was found that most differentially expressed nt-RNA (tumor vs control) were related to differential expression of the corresponding normal transcripts. However, nt-RNA were produced in 900 genes which were independent of higher production of the normal transcripts. In the example of KIRC, collection of 12 genes in the proteasome ubiquitination pathway standed out among the highly produced nt-RNA. This finding is very interesting as VHL-HIF1A is a key oncogenesis mechanism in KIRC and normal HIF1A degradation required proteasomal ubiquitination pathway. GO analysis was highly significant at p-value<4.11E-05. And the nt-RNA producing genes included PSMB4, PSMD14, PSMC6, PSMD13, PSMB1, VCP, ANAPC5, PSMA4, PSMD3, ANAPC7, OS9, GCLC. / Secondly, some nt-RNA retarded translation of the normal transcripts. By using proteome data, the relationship between quantity of nt-RNA unique tags and normal protein product were analyzed by ANOVA comparison of linear models. It was found that 422 nt-RNA unique tags influenced the expression of proteins, which suggested a potential biological action of these nt-RNA. PTEN also produced nt-RNA in KIRC and tumor cells with higher PTEN nt-RNA had a lower PTEN protein level (p-value of ANOVA comparison of linear models: 0.017). Survival analysis results showed that PTEN nt-RNA levels affected survival, which suggested that it can be used as biomarker for prognosis. Furthermore, survival analysis were done for other nt-RNA unique tags which affected protein expression using clinical data. / Thirdly, the application of nt-RNA as diagnostic markers and markers to define tumor origin in CUP were examined. nt-RNA were identified in different types of tumors. Here, only nt-RNA that were independent of the normal gene transcripts in term of differential expression were used as biomarkers. By comparing tumor samples with normal samples, nt-RNAs as diagnostic markers were detected. Unsupervised clustering was performed for these nt-RNAs and heat maps showed high degree of separation of tumor and normal samples. For studying tumor origin in CUP, in both cross-validation study in the training dataset (N=541) and independent sample set external validation (N=2462), a highly discriminating sets of nt-RNAs were defined for most cancers examined (400 nt-RNA seq. tags). Unsupervised clustering was performed for the 400 nt-RNA seq. tags and heat maps showed its power to define tumor origin in CUP. And then the significance of classifier formed by 400 nt-RNA seq. tags was measured by performing 100 resampling of the training set. The results for the 100 resampling showed that the correctly classified instance rate for training set had 96.4895% ± 0.75% (mean ± standard deviation); for validation set had 91.0239% ± 1.032611%. / In conclusion, this study showed nt-RNA can have important biological function and be used for various applications. It’s a potential biomarker for diagnosis and prognosis of diseases. And it can also be used to decide the origin site of tumors, which indicates that nt-RNA will provide great information for potential application in diagnosis of cancer and determining the origin in cancer of unknown primary site (CUP). [With diagram] / 無意介導的mRNA降解（NMD）是一種重要的保護機制，它可以防止錯誤的轉錄本，特別是含有提前終止密碼子的轉錄本。在經典的教學里，這種錯誤的轉錄本（這裡稱為無意介導的mRNA降解所靶向的轉錄本，記為nt-RNA）被認為是細胞轉錄過程中偶然產生的非特異性的副產物，它們很快被NMD清除，因此它們在細胞內的表達很少（即穩態時它們的表達量很少）。作為隨機的轉錄錯誤的一個副產物，它們通常被認為是沒有生物功能的。 / 通過分析大量的來自TCGA的RNA-seq的數據（超過4000個樣本，存儲空間超過50TB），我們發現一些基因的nt-RNA有很高的表達量，有的甚至超過同一個基因的正常轉錄本的表達量。 / 我們的假設是一些nt-RNA是由某個生物過程特定產生的，而不是偶然產生的。基於這一假設，本研究的目標有：（1）量化nt-RNA的表達（表達譜的調查）；（2）探索nt-RNA與蛋白質表達的關係（生物功能）；（3）尋找可以影響癌症預後的nt-RNA（生物功能）；（4）用nt-RNA作為癌症診斷的生物標記物（應用）；（5）識別可以用來區分原发灶不明的癌症的nt-RNA（應用）。 / 首先，通過基因的數據庫定義nt-RNA，并將這些nt-RNA與相應的正常的轉錄本進行比較，找到每個nt-RNA特有的標簽（包括系列的片段和剪接位点）。進而在RNA-seq數據所有的讀段中搜索這些nt-RNA特有的標簽并記數。通過這樣的搜索和記數，產生了每個nt-RNA特有標簽的讀段數目，而包含這些標簽的讀段就是NMD的靶標。本研究中使用的RNA-seq數據包含13種癌症的TCGA正常和癌症樣本，以及癌細胞系的樣本數據。 / 在腎癌的例子中，大多數差異表達（癌症與正常比較）的nt-RNA和它相應的正常的轉錄本的差異表達是有關聯的。然而，900个基因產生的nt-RNA與正常轉錄本的高表達是獨立的。我們發現與白酶體泛素化通路相關的12個基因高表達nt-RNA。這個發現是很有意思的，因為VHL-HIF1A是KIRC的一個重要的致癌機制，而正常的HIF1A的降解需要通過白酶體泛素化通路。白酶體泛素化通路在基因富集分析中是顯著的（p值<4.11E-05）。這12個基因分別是PSMB4，PSMD14，PSMC6，PSMD13，PSMB1，VCP，ANAPC5，PSMA4，PSMD3，ANAPC7，OS9，GCLC。 / 其次，一些nt-RNA可以降低正常轉錄本的翻譯。利用蛋白組數據，我們用ANOVA比較線性模型的方法研究了nt-RNA特有的標簽與正常的蛋白產物的關係。結果發現，422个nt-RNA特有的標簽影響蛋白質的表達，這說明nt-RNA具有潛在的生物作用。PTEN也在KIRC裡產生nt-RNA，PTEN的nt-RNA表達越高的樣本，含有越少的PTEN蛋白產物（ANOVA比較線性模型的p值=0.017）。生存分析的結果顯示PTEN的nt-RNA影響生存率，這說明PTEN的nt-RNA可以作為癌症預後的生物標記物。進一步，對其他的影響蛋白表達的nt-RNA特有的標簽也做了生存分析。 / 最後，我檢查了nt-RNA作為診斷標記物和用來定義原发灶不明的癌症（CUP）的起源的標記物的兩大應用。只有在差異表達方面獨立於正常轉錄本的那些nt-RNA會被用作生物標記物。通過比較癌症和正常的樣本，檢查了哪些nt-RNA可以作為診斷標記物。利用無監督的聚類分析和熱圖顯示了這些nt-RNA可以很明顯地將癌症和正常樣本分開。在研究原发灶不明的癌症（CUP）的起源中，通過對訓練集（N=541）和獨立的外部驗證集（N=2462）進行交叉驗證學習，定義了一個可以識別大多數癌症樣本的nt-RNA標簽集（400個nt-RNA特有的片段標簽）。無監督的聚類分析和熱圖顯示了用這些nt-RNA定義原发灶不明的癌症（CUP）的起源的能力。隨後，通過從訓練集的樣本隨機抽樣100次，檢查了由400個nt-RNA特有的片段標簽組成的分類器的顯著性。100次隨機抽樣的結果顯示：對訓練集，樣本準確分類率的均值和標準差分別是96.4895%和0.75%；對驗證集，樣本準確分類率的均值和標準差分別是91.0239%和1.032611%。 / 總之，本研究顯示了nt-RNA有重要的生物功能和多種應用。它是癌症診斷和預後的潛在的生物標記物。它也可以被用來決定癌症的原发灶，這意味著nt-RNA將會為癌症診斷和決定原发灶不明的癌症的原发灶的這些潛在應用提供很好的信息。[附圖] / Hu, Fuyan. / Thesis Ph.D. Chinese University of Hong Kong 2015. / Includes bibliographical references (leaves 173-211). / Abstracts also in Chinese. / Title from PDF title page (viewed on 12, October, 2016). / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only.

In humans, RNA polymerase II is the sole source of messenger RNAs that are ultimately translated into proteins and its transcriptional activity is highly regulated. Mechanisms have evolved to control which, when, and to what degree genes are transcribed. Because most cells have the same genome, control of transcription is essential in maintaining cellular identity. Misregulation of Pol II transcription is a hallmark of both cancer and retroviral infection. This research investigates the regulation of Pol II transcription and related co-transcriptional mRNA capping. Chromatin immunoprecipitation experiments were used to characterize the composition of nucleosomes and Pol II, DSIF and NELF occupancies at bidirectional promoters and enhancers. In collaboration with Alberto Bosque and Vicente Planelles, sequencing experiments were performed in a primary T cell model of HIV latency and a role for sequence-specific recruitment of STAT5 was established in HIV reactivation. In contrast, analysis of Myc binding in vitro and in cells demonstrated that transcription machinery played a major role in recruiting Myc to genomic sites. A precise method was also developed to detect polymerase-associated nascent transcripts in nuclei. The roles of Cdk7, a subunit of TFIIH that phosphorylates Pol II during initiation, were characterized by treatment of nuclear extracts and cells with THZ1, a recently developed covalent inhibitor with anti-cancer properties. Inhibition of Cdk7 was demonstrated to cause defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, and productive elongation. Capping of nascent RNAs was found to be spatially and temporally regulated in part by a previously undescribed THZ1-sensitive factor present in nuclear extract. THZ1 impacted pausing through a capping-independent block of DSIF and NELF loading. The P-TEFb-dependent transition into productive elongation was also inhibited by THZ1, likely due to misloading of DSIF. In vitro and sequencing methods were used to describe an extremely rapid and global transcriptional response to hydrogen peroxide. During periods of oxidative stress, termination was likely inhibited and Pol II accumulated at promoters and enhancers after as few as two minutes, and clearance of these polymerases required P-TEFb. In the presence of flavopiridol, a potent P-TEFb inhibitor, non-productive elongation was observed and a potential role for P-TEFb in termination was proposed.

Gene therapy has the potential to treat a wide variety of diseases. Delivering nucleic acids, such as DNA and mRNA, allows for the production of an aberrant or absent protein that is causing the disease. Delivery of genes via viruses is very efficient but falls short because of other issues. Nonviral delivery, on the other hand, struggles with efficiency but has advantages in terms of lack of immunogenicity, ease in production, and carrying capacity. DNA is much more stable than mRNA, and the protein production from DNA persists for a longer time. However, DNA delivered to cells must pass through the nuclear envelope to produce protein. Nuclear penetration with nonviral DNA delivery in vivo has not yet been accomplished. mRNA only needs to be delivered to the cytoplasm. Recent interest in nonviral delivery of mRNA has surged upward because delivery of mRNA to various cells in vivo has proven successful. Yet mRNA still struggles with nuclease stability, which is a major impediment toward efficient expression. A polyacridine PEG-peptide (PEG-peptide) has been previously used to stabilize DNA against nuclease hydrolysis by binding through ionic and intercalative interactions. Binding of PEG-peptide to DNA results in a PEGylated nanoparticle, or polyplex, and which protects the DNA. The same PEG-peptide was applied to mRNA. To increase the ability of PEG-peptide to bind through intercalation, a reverse complementary strand was hybridized to the mRNA, forming double stranded mRNA (dsmRNA). In a similar manner to DNA, complexing dsmRNA or single stranded mRNA (ssmRNA) with PEG-peptide resulted in formation of PEG-peptide polyplexes. A dsmRNA polyplex was much more resistant to ribonuclease challenge in vitro than a ssmRNA polyplex. The mRNA constructs were tested in vivo by hydrodynamic dosing. dsmRNA was found to be translationally competent by producing a high level of luciferase reporter enzyme in the liver of mice. When the reverse strand length was modified such that it hybridized with only the coding region, leaving the untranslated regions (UTRs) and poly(A) tail single stranded, the in vivo translatability (level of expression) and persistence (duration of expression) of dsmRNA was equivalent to that of ssmRNA. Full hybridization of the reverse strand with the coding region, the UTRs, and poly(A) tail resulted in a decrease of in vivo translatability. However, the circulatory stability (an in vivo measure of resistance to degradation in blood) was greatly increased when the reverse strand was fully hybridized. The persistence of expression of exogenously delivered mRNA is poor in comparison to DNA. The first step in mRNA decay in the cytoplasm is predominantly poly(A) tail shortening, or deadenylation. To address the persistence issue, mRNA with nonadenosine extensions at the 3’ end of the poly(A) tail was synthesized to inhibit deadenylation-dependent mRNA decay. However, increase of the length of tail extension resulted in a concomitant overall decrease in translatability and no increase in persistence. Hybridization of a DNA oligo to the origin of the tail extension activated endogenous RNase H, cleaving the tail extension, exposing the poly(A) tail, and reactivating the mRNA for high level translation, although no increase in persistence was seen with this strategy. A structured tail extension consisting of two human β-globin 3’UTR sequences increased persistence but also decreased overall translatability. Enzymatic poly(A) tailing of this structured tail extension brought back the translatability but simultaneously lost the persistence gain. While this study on poly(A) tail extension mRNA did not produce a highly active mRNA that had increased persistence, its results may be applicable toward other gene therapy applications. Other efforts to increase the metabolic stability or persistence of mRNA were pursued. Scavenger receptors on resident liver macrophages remove polyplexes from the blood by phagocytosis. Saturation of the scavenger receptors by coadministration of a scavenger receptor inhibitor resulted in increased circulatory stability of dsmRNA. However the scavenger receptor inhibitor was toxic in mice. Another effort to increase the persistence of gene expression in vivo was utilizing an autogene. Autogenes are able to drive the expression of a DNA-based gene outside of the nucleus. In its final form, the autogene did not produce expression. It is an exciting time to be in the field of mRNA gene therapy. Hopefully the research presented in this thesis will factor in to the knowledge base that can treat and cure human diseases.