Assembly of the SARS-CoV-2 transcriptome through nanopore ReCappable sequencing
About Camilla Ugolini
Camilla Ugolini is a Ph.D. student in Computational Biology at the IIT institute under the supervision of Dr. Leonardi and Dr. Nicassio. She graduated in physics and then focused on bioinformatics. Camilla is currently pursuing various projects centred around nanopore direct RNA sequencing, applied to diverse biological questions such as the transcriptional and epitranscriptional landscape of SARS-CoV-2, the profiling of Triple Negative Breast Cancer cells and the detection and quantification of transposable elements in human samples.
After the breakout of the SARS-CoV-2 pandemic, the need for comprehensive characterization of its transcriptional landscape became clear.
According to the prevailing model, the transcription of SARS-CoV-2 leads to the generation of subgenomic RNAs (sgRNAs) having a common 5’ leader sequence fused to different “body” sequences containing an ORF.
We used Nanopore ReCappable sequencing (NRCeq), a recent experimental strategy that exchanges the 5’ RNA cap for a modified cap linked to an adapter, to identify full-length sgRNAs and build an assembly of SARS-CoV-2 transcriptome that recovers the majority of annotated ORFs.
We also quantified sgRNA expression across multiple isolates and identified multiple modification sites which, given the increasing evidence supporting roles for RNA modifications in regulating RNA properties, could provide important insights into new potential vulnerabilities in the biology of SARS-CoV-2.