The RNA-binding protein (RBP) and Hu/ELAV family member HuD regulates mRNA metabolism of genes that encode proteins involved in neuronal differentiation, learning and memory, and certain neurological diseases. Given the important functions of HuD in a variety of processes, we set out to characterize the 5’ genomic region of the mammalian HuD gene and determine the mechanisms that regulate its mRNA expression in neurons using P19 cells and mouse brain as models. Bioinformatic and 5’RACE (rapid amplification of cDNA ends) analyses of the HuD 5’ genomic flanking region identified eight conserved leader exons (E1s), two of which are novel. Expression of all E1 variants was established in differentiating P19 cells, mouse embryonic (E14.5) and adult brains. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in differentiating neurons. Sequential deletion of the 5’ regulatory region upstream of the predominantly expressed E1c variant revealed a well-conserved 400 bp DNA region that contains five E-boxes and is capable of directing expression of HuD specifically in neurons. Using electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitations (ChIPs), and E1c 5’ regulatory region (RR) deletion and mutation analysis, we found that two of these E-boxes are targeted by neurogenin 2 (NGN2/NEUROG2) and that this mechanism is important for induction of HuD mRNA in neurons. Additional deletion and mutation of the E1c 5’ RR revealed that putative cis-acting elements for Kruppel-like factors (KLFs) and nuclear DEAF-1-related (NuDR) transcription factors also positively regulate transcription of HuD. Together, our findings reveal that the intricate transcriptional regulation of mammalian HuD involves eight leader exons and potentially alternate promoters. We further demonstrate that transcription of HuD requires neuron-specific control by NGN2 and possibly KLF and NuDR transcription factors. To our knowledge, this is the first study to identify transcriptional events that positively regulate expression of HuD.

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For many human protein-coding genes, alternative cleavage and polyadenylation (APA) of pre-mRNA generates distinct 3' untranslated regions (3'UTRs) with differing regulatory potential. Widespread 3'UTR shortening via APA occurs in proliferative cell states, including cancer, where it can lead to oncogene overexpression. There has therefore been significant interest in identifying factors which influence poly(A) site choice in different physiological states. The multi-subunit human cleavage factor I complex (CFIm), a core component of the mammalian pre-mRNA cleavage machinery, has been identified as a potential master regulator of APA, as its depletion leads to widespread 3'UTR shortening. However, mechanistic understanding of how CFIm influences poly(A) site selection, and how its activity is regulated, is lacking. In this work, gene editing was used to generate cell lines with substantial, permanent depletion of the 25 kDa or 68 kDa subunits of CFIm (CFIm25 and CFIm68), which exhibited the expected 3'UTR shortening for representative transcripts. Reversal of this 3'UTR shortening by CFIm25 or CFIm68 re-expression provided the basis for a complementation assay, which allowed various aspects of CFIm25 and CFIm68 function to be investigated in vivo. The capacity of CFIm25 to recognise UGUA RNA sequences was shown to make an important contribution to poly(A) site selection transcriptome-wide, and a novel function for the C-terminal arginine/serine-rich (RS domain) of CFIm68 in poly(A) site selection was identified. The potential contribution of CFIm post-translational modification (PTM) to APA regulation was also explored. Novel acetylation sites on CFIm25 and CFIm68 were identified, as well as extensive serine phosphorylation in the CFIm68 RS domain. Complementation analysis revealed that phosphomimetic mutations in this RS domain inhibited distal poly(A) site selection, suggesting a potential role for CFIm68 phosphorylation in APA regulation. Taken together, the findings presented here provide insights into several important determinants of CFIm function, and the complementation assay developed provides a useful tool for future investigations.

Made available in DSpace on 2018-08-02T00:16:24Z (GMT). No. of bitstreams: 1 tese_6085_IRANY RODRIGUES PRETTI.pdf: 1820028 bytes, checksum: 206c5b4515936d11e0d571040d9689c8 (MD5) Previous issue date: 2012-02-29 / RESUMO O maracujazeiro é cultivado em quase todo o território brasileiro. O Estado do Espírito Santo atualmente ocupa o quarto lugar em produção no país. A produção capixaba, de Passiflora edulis, está em expansão, tendo em vista que nos últimos anos houve um aumento na área plantada de maracujazeiro de 500 ha, em 1990, para 2.429 ha, em março de 2008, atingindo em dezembro de 2010, 2.800 ha plantados. Contudo, a maior parte da produção capixaba ainda se concentra na região norte do Estado, com destaque para os municípios de Jaguaré e Sooretama. Apesar dos números mostrarem avanços na produção dessa frutífera, o Espírito Santo é caracterizado por solos ácidos e alto teor de alumínio. Dentre as respostas desencadeadas pela exposição ao alumínio estão: inibição do crescimento radicular, inibição da divisão celular, deficiência de nutrientes, além da ativação de rotas de sinalização e alterações em nível de proteínas e transcritos de RNA. Dessa forma, torna-se fundamental o estudo de componentes do sistema de defesa antioxidativo do maracujazeiro cultivado sob exposição ao alumínio. As EROs podem representar grave ameaça à célula, sendo uma das respostas aos estresses ambientais, como a toxidez por alumínio. Contudo, poucos trabalhos têm relatado os efeitos do Al na parte aérea da planta. Por isso, o objetivo deste trabalho foi verificar a resposta o sistema antioxidante de P.edulis sob tais condições. O estudo do estresse oxidativo induzido por alumínio demonstrou que a expressão do gene Cat e Sod foi aumentada nas plantas em solução nutritiva, e somente na cv. FB100 esse aumento foi acompanhado pelo incremento da atividade enzimática de SOD, o que indica maior eficiência desta na remoção de EROs. As plantas cultivadas em campo demonstraram que a expressão das enzimas antioxidantes na lavoura com alto teor de alumínio não estava ativada no momento da coleta, apesar da elevada atividade de SOD e APX. Esta resposta possivelmente foi determinada pelo tempo prolongado ao qual as plantas estavam expostas ao estresse.

Abstract In malignancies many alterations involving matrix macromolecule synthesis, secretion and assembly into basement membranes (BMs) as well as their degradation are present. The most important groups associated with matrix turnover are matrix metalloproteinases (MMPs) and their inhibitors (TIMPs). In this study altogether 285 tissue samples were investigated comprising various malignant epithelial tumors and normal tissue structures, in which the distribution of different laminin chains was studied immunohistochemically. Laminin α5, β1 and γ1 were detected almost in all the BMs studied including normal tissues and malignancies, whereas α1 chain of laminin was present only in certain BMs. Laminin γ2 chain was solely expressed by epithelial BMs and was present in intracellular space especially in individual carcinoma cells infiltrating in the tumor stroma and in tumor cells in close contact with BM zone. Generally epithelial tumors contained quite well-formed BMs around their tumor clusters, except for infiltrative breast carcinoma and diffuse type gastric carcinoma. In situ hybridization revealed that only epithelial cells contained mRNAs for laminin α1 and γ2 chains, whereas laminin β1 chain and α1(IV) collagen were synthesized mainly by stromal cells. mRNA for MMP-2 was produced mainly by stromal cells in hepatocellular carcinoma of liver (HCC) and pancreatic adenocarcinoma, whereas MMP-9 and MT1-MMP were equally synthesized by carcinoma cells and cells of tumor stroma. However, in HCCs of grade III carcinoma cells predominated in their MT1-MMP expression. All three MMPs were immunolocalized to malignant epithelial cells and showed variably stromal cell positivity. Statistically mRNA synthesis for MT1-MMP was significantly associated with the shortened survival of patients with HCC (P ≤ 0.01). TIMP-1-3 mRNA, and especially TIMP-3, expressions in normal endometrium were significantly increased in endometrial stromal cells towards the secretory phase. In various endometrial hyperplasias TIMPs and MT1-MMP expressions were quite comparable to those seen in proliferating endometrium. In endometrial adenocarcinomas their expressions were significantly increased and the most intensified mRNA expressions were seen in grade III adenocarcinomas. Especially TIMP-3 and MT1-MMP mRNAs were synthesized by carcinoma cells. The results indicate that epithelial malignancies are capable of active synthesis and assembly of BM macromolecules. Simultaneous matrix synthesis and degradation seen in malignancies suggest that the mechanisms involved in matrix turnover are not lost during malignant transformation. mRNA synthesis for MMPs and TIMPs is generally increased in epithelial malignancies. The results therefore strongly support the concept that MMPs have an active role in carcinoma cell invasion.

The RNA-binding protein (RBP) and Hu/ELAV family member HuD regulates mRNA metabolism of genes that encode proteins involved in neuronal differentiation, learning and memory, and certain neurological diseases. Given the important functions of HuD in a variety of processes, we set out to characterize the 5’ genomic region of the mammalian HuD gene and determine the mechanisms that regulate its mRNA expression in neurons using P19 cells and mouse brain as models. Bioinformatic and 5’RACE (rapid amplification of cDNA ends) analyses of the HuD 5’ genomic flanking region identified eight conserved leader exons (E1s), two of which are novel. Expression of all E1 variants was established in differentiating P19 cells, mouse embryonic (E14.5) and adult brains. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in differentiating neurons. Sequential deletion of the 5’ regulatory region upstream of the predominantly expressed E1c variant revealed a well-conserved 400 bp DNA region that contains five E-boxes and is capable of directing expression of HuD specifically in neurons. Using electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitations (ChIPs), and E1c 5’ regulatory region (RR) deletion and mutation analysis, we found that two of these E-boxes are targeted by neurogenin 2 (NGN2/NEUROG2) and that this mechanism is important for induction of HuD mRNA in neurons. Additional deletion and mutation of the E1c 5’ RR revealed that putative cis-acting elements for Kruppel-like factors (KLFs) and nuclear DEAF-1-related (NuDR) transcription factors also positively regulate transcription of HuD. Together, our findings reveal that the intricate transcriptional regulation of mammalian HuD involves eight leader exons and potentially alternate promoters. We further demonstrate that transcription of HuD requires neuron-specific control by NGN2 and possibly KLF and NuDR transcription factors. To our knowledge, this is the first study to identify transcriptional events that positively regulate expression of HuD.

The U5 snRNP is a major component of the yeast spliceosome, being part of the U4/U6.U5 tri-snRNP, the precatalytic spliceosome and the catalytically activated spliceosome. The U5 snRNP includes, at its heart, the U5 snRNA which contains the invariant Loop 1 that functions in tethering and aligning exons during splicing. The major protein components of the U5 snRNP are the highly conserved Prp8p, the GTPase Snu114p and the helicase Brr2p. These proteins and the U5 snRNA are integral in forming the active site of the spliceosome and regulating the dynamic changes of the spliceosome. The first part of this study aimed to express and purify specific domains of Snu114p to define the structure and function of Snu114p. The N-terminal region of Snu114p was successfully expressed and purified from bacteria. Addition of the Snu114p N-terminal fragment to in vitro splicing assays resulted in a first step splicing defect, indicating a role for the N-terminus in pre-mRNA splicing. NMR studies revealed that the N-terminus of Snu114p exists as an unstructured protein domain. Mutagenesis indicated that the N-terminus of Snu114p is tolerant to mutation. A novel genetic interaction between amino acids in the N-terminus of Snu114p and the 3’ side of the U5 snRNA IL1 was identified. It is proposed here that the N-terminus of Snu114p functions to stabilise interactions of Snu114p with other proteins or snRNAs, possibly the U5 snRNA. Alternatively, the N-terminus of Snu114p may form intramolecular interactions with other regions of Snu114p to regulate Snu114p function in pre-mRNA splicing.Prp8p, Snu114p and Brr2p are known to form a stable complex but their interactions with the specific domains of the U5 snRNA are not known. The second part of this study aimed to investigate the association of Brr2p, Snu114p and Prp8p with the U5 snRNA. Mutants of the U5 snRNA were constructed in the conserved Loop 1 and the Internal Loop 1 (IL1). The influences of the U5 snRNA mutations on interactions of Prp8p, Snu114p or Brr2p with the snRNA were investigated. It was revealed that Loop 1 and both sides of IL1 of the U5 snRNA are important in association of Brr2p, Snu114p and Prp8p. Mutations in the 3’ side of IL1 drastically reduce association of Brr2p, Snu114p and Prp8p with the U5 snRNA, highlighting this region as a potential ‘protein docking’ site within the U5 snRNP. Differences seen in the associations of Brr2p, Snu114p and Prp8p with U5 snRNA mutations demonstrate that although there are intimate interactions between Brr2p, Snu114p and Prp8p, they do not associate with the U5 snRNA as a tri-protein complex. Genetic screening of BRR2 and U5 snRNA mutants reveals an interaction between the N-terminal half of Brr2p and the 3’ side of U5 snRNA IL1. This supports the proposed ‘protein docking’ site at the 3’ side of the U5 snRNA IL1.Data presented in this study increases our understanding of the regions in the U5 snRNA required for association of the essential U5 snRNP proteins, Brr2p, Snu114p and Prp8p, and goes some way to elucidating the organisation of essential proteins within the U5 snRNP.

Endocannabinoid signaling is well studied in mammals and known to be involved in numerous pathological and physiological processes. Fatty acid amide hydrolase (FAAH) terminates endocannabinoid signaling in mammals. In Physcomitrella patens, we identified nine orthologs of FAAH (PpFAAH1 to PpFAAH9) with the characteristic catalytic triad and amidase signature sequence. Kinetics of PpFAAH1 showed specificity towards anandamide (AEA) at 37°C and pH 8.0. Further biophysical and bioinformatic analyses revealed that, structurally, PpFAAH1 to PpFAAH4 were closely associated to the plant FAAH whereas PpFAAH6 to PpFAAH9 were more closely associated to the animal FAAH. A substrate entry gate or ‘dynamic paddle’ in FAAH is fully formed in vertebrates but absent or not fully developed in non-vertebrates and plants. In planta analysis revealed that PpFAAH responded differently with saturated and unsaturated N-acylethanolamines (NAEs). In vivo amidohydrolase activity showed specificity associated with developmental stages. Additionally, overexpression of PpFAAH1 indicated the need for NAEs in developmental transition. To understand and identify key molecules related to endocannabinoid signaling in P. patens, we used high-throughput RNA sequencing. We analyzed temporal expression of mRNA and long non-coding RNA (lncRNA) in response not only to exogenous anandamide but also its precursor arachidonic acid and abscisic acid (ABA, a stress hormone). From the 40 RNA-seq libraries generated, we identified 4244 novel lncRNAs. The highest number of differentially expressed genes (DEGs) for both mRNA and lncRNA were detected on short-term exposure (1 h) to AEA. Furthermore, gene ontology enrichment analysis showed that 17 genes related to activation of the G protein-coupled receptor signaling pathway were highly expressed along with a number of genes associated with organelle relocation and localization. We identified key signaling components of AEA that showed significant difference when compared with ABA. This study provides a fundamental understanding of novel endocannabinoid signaling in early land plants and a future direction to elucidate its functional role.

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