Dr

Heejung Shim

Accurate identification of mRNA alternative splicing using Oxford Nanopore sequencing

The pre-mRNA alternative splicing events enable a single gene to produce different proteins in eukaryotes, and they have been shown to affect various gene functions, and eventually disease. The alternative splicing can not only add or skip entire exons, but can also vary exon boundaries by selecting different nucleotides as splice sites. Oxford Nanopore sequencing produces long reads that have natural advantages for characterising alternative splicing events. Nanopore sequencing records changes in electrical current when a DNA or RNA strand is traversing through a pore. This raw signal, known as a squiggle, is then basecalled by computational methods. However, due to the high error rate in the basecalling process, it is challenging to accurately identify exon boundaries using the basecalled sequences. In this talk, I will introduce new methods that use the squiggle to characterise the exon boundaries, in addition to the basecalled sequences.