We developed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) followed by high-throughput sequencing to study protein-RNA interactions. We developed algorithms and the iCount pipeline for mapping iCLIP sequence reads to the human genome, quality-control filtering, removal of PCR duplicates and quantification of binding using random barcodes, generation of cross-link maps, identification of significant clusters of cross-links and analysis of enriched pentanucleotides. We then studied the positioning of hnRNP C particles and their role in alternative splicing.
COBISS.SI-ID: 7800916
We used iCLIP and the computational pipeline iCount to study the role of TIA1 and TIAL1 proteins in alternative splicing. Studies of splicing regulation generally focus on RNA elements located in the proximity of alternative exons. For the two mentioned proteins we have shown that observing the recognition of distal regulatory sites in the preceding 5’ splice sites may play an important role in fully understanding the regulation of alternative splicing.
COBISS.SI-ID: 8022356