Analysis and regulation of alternative splicing in the pig infarted myocardium

• Autores: Girolamo Giudice
• Directores de la Tesis: Carlos Torroja Fungairiño (dir. tes.), Enrique Lara Pezzi (dir. tes.)
• Lectura: En la Universidad Autónoma de Madrid ( España ) en 2017
• Idioma: inglés
• Tribunal Calificador de la Tesis: Carmelo Bernabeu Quirante (presid.), Miguel Manzanares Fourcade (secret.), Fátima Al-Shahrour (voc.), Gonzalo Gómez López (voc.), Fátima Sánchez Cabo (voc.)
• Programa de doctorado: Programa Oficial de Doctorado en Bioquímica, Biología Molecular, Biomedicina y Biotecnología (Biociencias Moleculares)
• Materias:
  • Ciencias de la vida
    • Biología molecular
• Enlaces
  • Tesis en acceso abierto en: Biblos-e Archivo
• Resumen

  • In all eukaryotes, pre-mRNA splicing is a necessary step for protein synthesis. Pre-mRNA splicing is mediated by the spliceosome, a dynamic complex of 100/150 proteins and RNAs, which is assembled de novo at every splicing event. The same pre-mRNA can be spliced in different ways generating different isoforms that potentially regulate gene expression or affect protein structure, function, or localisation. RNA binding proteins, finely regulate this process by recognising short sequences located in the exons or in the neighbour introns that favour the inclusion or the exclusion of an exon in the mature mRNA.

    The advent of RNA sequencing has allowed the investigation of the splicing patterns and concurrently the quantification of mRNA abundance underlying a phenotype. Currently, the interpretation of the changes in the splicing patterns and their regulation represents one of the major challenges in biomedical research.

    To collect in a unique resource all the regulatory elements and the RNA-binding proteins that were spread across different repositories, we developed a database named ATtRACT. Subsequently, we investigated the impact of alternative splicing in the pig infarcted myocardium. The analysis focused on four different cell types, cardiomyocytes, fibroblasts, endothelial cells, and macrophages at three different time points before and after infarction. We employed two distinct pipelines that allowed us to detect isoform switches after myocardial infarction, and to identify, thanks to the data available in ATtRACT, the RNA binding proteins and associated motifs that potentially regulate the alternative splicing.

    The analysis of the biological impact of large gene/protein sets is currently an open issue in bioinformatics. A widely-adopted procedure involves the enrichment analysis. Here, we developed a new functional enrichment analysis method, called MAGNETO. The main aim of MAGNETO was to gain more insight into of the biological processes underlying a phenotype by employing protein-protein interaction networks.

    Our results show that ATtRACT represents an invaluable resource for all the researchers involved in the study of RNA binding proteins. ATtRACT adds 192 motifs not available in any other database by retrieving the information buried in the Protein Data Bank. Two hundred and ten genes were detected as alternatively spliced after myocardial infarction in cardiomyocytes, fibroblast, endothelial cells, and macrophages. Forty-one were also detected at the protein level. Moreover, our findings suggest that alternatively spliced isoforms could be of great use to develop novel therapeutic approaches to avoid adverse cardiac remodelling and improve cardiac repair. Finally, our results confirm that MAGNETO allows to gain more overrepresented terms with respect to the standard enrichment analysis and to generate new hypotheses on the phenotype under investigation.