(FBIOyF) Departamento de Ciencias Biológicas
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Examinando (FBIOyF) Departamento de Ciencias Biológicas por Autor "Armas, Pablo"
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Ítem Acceso Abierto Beyond the binding site: In vivo Identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development(Public Library of Science, 2013-05-07) Armas, Pablo; Margarit, Ezequiel; Mouguelar, Valeria; Allende, Miguel L.; Calcaterra, Nora B.CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.Ítem Acceso Abierto CNBP controls transcription by unfolding DNA G-quadruplex structures(Oxford University Press, 2019-06-20) David, Aldana P.; Pipier, Angélique; Pascutti, Federico; Binolfi, Andrés; Weiner, Andrea María Julia; Challier, Emilse; Heckel, Sofía; Calsou, Patrick; Gomez, Dennis; Calcaterra, Nora B.; Armas, PabloÍtem Acceso Abierto G-quadruplexes as novel cis-elements controlling transcription during embryonic development(Oxford University Press, 2016-01-14) David, Aldana P.; Margarit, Ezequiel; Domizi, Pablo; Banchio, Claudia; Armas, Pablo; Calcaterra, Nora B.G-quadruplexes are dynamic structures folded in G-rich single-stranded DNA regions. These structures have been recognized as a potential nucleic acid based mechanism for regulating multiple cellular processes such as replication, transcription and genomic maintenance. So far, their transcriptional role in vivo during vertebrate embryonic development has not yet been addressed. Here, we performed an in silico search to find conserved putative G-quadruplex sequences (PQSs) within proximal promoter regions of human, mouse and zebrafish developmental genes. Among the PQSs able to fold in vitro as G-quadruplex, those present in nog3, col2a1 and fzd5 promoters were selected for further studies. In cellulo studies revealed that the selected G-quadruplexes affected the transcription of luciferase controlled by the SV40 nonrelated promoter. G-quadruplex disruption in vivo by microinjection in zebrafish embryos of either small ligands or DNA oligonucleotides complementary to the selected PQSs resulted in lower transcription of the targeted genes. Moreover, zebrafish embryos and larvae phenotypes caused by the presence of complementary oligonucleotides fully resembled those ones reported for nog3, col2a1 and fzd5 morphants. To our knowledge, this is the first work revealing in vivo the role of conserved G-quadruplexes in the embryonic development, one of the most regulated processes of the vertebrates biology.Ítem Acceso Abierto Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes(Oxford University Press, 2023-11-01) Lorenzatti, Agustín; Piga, Ernesto José; Gismondi, Mauro; Binolfi, Andrés; Margarit, Ezequiel; Calcaterra, Nora B.; Armas, PabloGuanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases’ onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer’s disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases’ onset, and could be novel targets for diagnosis and drug design in precision medicine.Ítem Acceso Abierto Insights into vertebrate head development: from cranial neural crest to the modelling of neurocristopathies(UPV/EHU Press, 2020-08-27) Weiner, Andrea María Julia; Coux, Gabriela; Armas, Pablo; Calcaterra, Nora B.