Advancement: Investigating RNA modifications in cancer through site-directed A-to-I editing for inosine identification in nvRNA sequencing

Speaker Name: 
Alison Tang
Speaker Title: 
PhD Student
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Tuesday, July 31, 2018 - 9:00am
End Time: 
Tuesday, July 31, 2018 - 11:00am
Biomedical Sciences, Room 200
Angela Brooks

Abstract:  There are upwards of 100 distinct mRNA modifications that can alter mRNA stability, activity, and localization. One such RNA modification is the deamination of an adenosine to form an inosine, a modification that has been implicated in several cancers. To systematically study A-to-I editing at an isoform-level, I propose to generate native RNA sequencing data for the identification of inosines in a sequence context-independent manner. Nanopore native RNA (nvRNA) sequencing resolves RNA molecules by applying a voltage across a membrane embedded with nanopores, causing genetic material to translocate through the pores. Blockage of the pore creates characteristic changes in current that can be measured and decoded as sequence. nvRNA sequencing confers several advantages in that by directly sensing the full RNA without RT/PCR, modification and isoform-level data are preserved. I propose to use a Cas13b-ADAR2 fusion to create site-directed A-to-I edits with high specificity. Using this data, I will develop computational methods for the identification of inosines as anomalies and for accurate definition of inosine-specific isoforms in nvRNA data. Using models built from my inosine nvRNA data, I then plan to detect A-to-I editing using nvRNA sequencing in LUAD cells, where A-to-I editing of genes is associated with a more proliferative state. Ultimately, my project will help lay the foundation for learning any RNA modification in the nanopore using Cas13b fusions.