Characterization of the circRNome in the heart A bioinformatic approach

In this thesis, we performed studies that add new insights into the biology of circular RNAs (circRNAs) in the heart. We characterized the human circRNA landscape in the heart from RNA-sequencing data and identified thousands of circRNAs, with some of them regulated in disease. We found that an unusually high number of circRNAs are produced from the Titin (TTN) gene and show that RNA binding motif 20 (Rbm20)-dependent exon skipping within Ttn's I-band region is associated with circRNA formation. We performed RNA-sequencing on mouse (wildtype and Rbm20 knockout) hearts to investigate Rbm20-regulated circRNA production. We show that the tight correlation between Rbm20-mediated exon skipping and circRNA formation observed in the Ttn gene does not appear a common mechanism for Rbm20 target genes, indicating that circRNA formation is not a general function of Rbm20. In addition, integrated analyses of alternative splicing and circRNA production in human and mouse hearts revealed that alternative splicing only accounts for a small proportion (~10%) of the circRNAs, with the vast majority of the circRNAs arising from constitutive exons indicating that these circRNAs are generated at the expense of their linear counterpart. Finally, we present circRNAprofiler, an R-based computational framework for a comprehensive in silico analysis of identified circRNAs. CircRNAprofiler covers different aspects of circRNA analysis ranging from differential expression analysis, genomic context, evolutionary conservation, biogenesis to functional analysis. The results obtained by running the circRNA analysis workflow implemented by circRNAprofiler can serve as a starting point for further investigation in the role of specific circRNAs in any physiological and pathological condition.