Regulated Gene Expression (rGE) and Alternative Splicing (rAS) are two of the main mechanisms contributing to tissue-phenotypic diversity within and between species. In this thesis, we aim at characterizing rGE and rAS patterns impacting tissue-specific transcriptomes throughout ~600 million years of bilaterian evolution. Our work revolves around (1) a vast RNA-seq dataset covering eight tissues across a symmetric phylogeny of twenty bilaterian species (eight vertebrates, eight insects and two pairs of outgroups); and (2) the exclusive focus on bilaterian-conserved genes. First, we identify ancestral tissue-specific rGE patterns, together with parallel, convergent and divergent evolutionary trajectories between and within vertebrates and insects. Second, we develop a software to infer exon orthologies at any evolutionary distance, a crucial prerequisite for rAS evolutionary analyses. Third, we characterize a compendium of tissue-specific exons across all species. Finally, we compare rGE- and rAS- regulated genes, extracting unique features associated with each type of tissue-specific regulation.
(Universitat Pompeu Fabra, 2023-05-25T14:47:39Z) Mantica, Federica; Irimia Martínez, Manuel; Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida
