Browsing by Issue Date, starting with "2019-01-24"
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- NMD-associated proteins predicted by an integrative network approachPublication . Nogueira, Gonçalo; Pinto, Francisco; Romão, LuísaThe mechanism of nonsense-mediated decay (NMD) selectively degrades mRNAs carrying a premature translation-termination codon and regulates the abundance of a large number of physiological mRNAs that encode full-length proteins. Although this complex process has been extensively studied along the years, the interactions and connectivity among NMD players is not completely understood. Additionally, some NMD mechanistical aspects suggest missing roles that can be played by proteins still not reported as involved in this pathway. To tackle this hypothesis, we developed a network-based approach to predict new proteins involved in NMD. Our approach explores the ability of proteins to bridge related processes, while integrating data regarding protein-protein interactions, co-expression and co-regulation by miRNAs and transcription factors. We found that known NMD-factors have physical, regulatory and co-expression interaction signatures with related processes (mRNA translation, mRNA splicing, mRNA degradation and mRNA transport), which can be used to distinguish them from other proteins. We computed a scoring algorithm to rank NMD-neighbors according to the similarity to these signatures, generating a list of NMD candidates, that we aim to validate experimentally. Interestingly, some candidates were recently studied in NMD context and showed promising results. Furthermore, a cross-validation analysis indicated the robustness of the predictions provided by our method. We propose that such approach can be applied to find molecular bridges between related biological processes and generate novel hypotheses about the molecular mechanisms co-regulating these phenomena.
- Translational regulation mediated by upstream open reading frames im PERK mRNAPublication . Fernandes, Rafael; Romão, LuísaGenome-wide studies pointed out translation as a major regulator of gene expression, being a key post-transcriptional mechanism by which cells rapidly change their gene expression pattern in response to diverse stimuli. Upstream open reading frames (uORFs) are examples of cis-acting elements that can regulate translation initiation. A uORF is defined as a coding sequence located within the 5’untranslated region (5’UTR) of an mRNA and is typically considered a repressor of main ORF (mORF) translation. This can be due to the recognition of the uORF start codon by the preinitiation complex. In this case, when the translating ribosome encounters the uORF stop codon, the translation machinery disassembles, avoiding mORF translation if the ribosome cannot reinitiate at the main start codon. ATF4, CHOP and GADD34 are stress-response proteins encoded by uORF-harboring transcripts with translation repression activity, which is responsible for maintaining a low expression of these proteins in normal conditions. However, when ER stress occurs, the unfolded protein response (UPR) is activated and eIF2α is phosphorylated by PERK. In these cases, the availability of the preinitiation complex is reduced, favoring translation of the mORFs. The stress-response proteins are therefore up regulated, triggering a cascade of events aiming stress resolution and cell survival. In this work we intended to determine if PERK is regulated at the translational level in normal and ER stress conditions. We have validated the annotated sequence of PERK 5’UTR using 5’RACE, and we have selected uORFs based on ribosome profiling data already available. Then, we have cloned the 5’UTR into a reporter plasmid, in frame with firefly luciferase ORF. Using site-directed mutagenesis, we have made constructs with mutated uORFs to evaluate their impact in translation efficiency. Our data suggest that the uORFs have a repressive effect in mORF translation, and we are now dissecting the mechanisms that drive this regulation.
- Mechanistic aspects of nonsense-mediated mRNA decay in human cellsPublication . Costa, Paulo J. da; Menezes, Juliane; Saramago, Margarida; García-Moreno, Juan F.; Santos, Hugo A.; Gama-Carvalho, Margarida; Arraiano, Cecília M.; Viegas, Sandra C; Romão, LuísaThe nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs carrying a premature translation-termination codon but also regulates the abundance of a large number of physiological RNAs that encode full-length proteins. NMD results from improper translation termination at stop codons, and thus, it is a cytoplasmic and translation-dependent process. In human cells, mRNA decay inherent to NMD involves an endonucleolytic cleavage near the stop codon and exonucleolytic degradation from both 5’ and 3’ ends. This is done by a process not yet completely understood that recruits decapping and 5’-to-3’ exonuclease activities, as well as deadenylating and 3’-to-5’ exonuclease exosome activities. In yeast, DIS3/Rrp44 protein is the catalytic subunit of the exosome, but in humans, there are three known paralogues of this enzyme: DIS3, DIS3L1, and DIS3L2. However, DIS3L2 exoribonuclease activity is independent of the exosome. DIS3L1 and DIS3L2 exoribonucleases localize in the same compartment where NMD occurs, however little is known about their role in this process. In order to unveil the role of DIS3L2 in NMD, we performed its knockdown in HeLa cells and measured the mRNA levels of various natural NMD-targets. Our results show that some NMD-targets accumulate in DIS3L2-depleted cells. In addition, mRNA half-life analysis indicated that these NMD-targets are direct DIS3L2 substrates. Besides, we observed that DIS3L2 acts over full-length transcripts, being DIS3L2-mediated decay dependent on the activity of the terminal uridylyl transferases (TUTases) Zcchc6/11 (TUT7/4). Together, our findings establish the role of DIS3L2 and uridylation over human NMD-targets.
- Functional networks of DIS3L2 in cancer and NMDPublication . García-Moreno, Juan; da Costa, Paulo J; Menezes, Juliane; Pereira, Marcelo; Gama-Carvalho, Margarida; Matos, Paulo; Romão, LuísaIn the flow of information from DNA to mRNA to proteins, mRNAs undergo a number of processing steps, since they are synthesized in the nucleus, until they are translated in the cytoplasm. Eukaryotic cells tightly control the fidelity of this process, via quality control pathways, among them, the nonsense-mediated mRNA decay (NMD). NMD recognizes and degrades mRNAs harboring premature translation-termination codons (PTCs), protecting the cell from potentially harmful truncated proteins. However, NMD can also regulate normal and fully functional mRNA levels, arising as a surveillance and a gene expression regulation pathway. A new branch of the NMD pathway is starting to be revealed, which is characterized by the involvement of the DIS3L2 3’ to 5’ exoribonuclease. This protein, has special relevance, given its exosome-independent action and its uridylation-mediated decay. In addition, mutations on this ribonuclease, induce deregulation of cell-cycle genes leading to a faster cell growth and decreased chromosome stability, while DIS3L2 downregulation enhances cancer stem cell properties. Several lines of evidence point to an oncogenic role of DIS3L2 and its mediated decay over a number of NMD targets, however further research is needed to unveil the mechanism by which this nuclease is involved in NMD and how it mediates cancer related processes. In this project, we aim to analyze how DIS3L2 and uridylation regulate the human transcriptome, in order to shed light on how this ribonuclease is related to NMD and how its deregulation contributes to tumorigenesis. For this purpose, high-throughput mRNA sequencing has been performed in the SW480 colorectal cancer cell line depleted of DIS3L2 or DIS3L2 plus terminal uridylyl transferases (TUTases), TUT4 and TUT7. Preliminary results show gene ontology enrichment in molecular functions and biological processes related with cancer.