Leena Putzeys from KU Leuven, Belgium spoke at London Calling 2022 about “Unlocking the transcriptomic architecture of bacterial viruses with ONT-cappable-seq.” Putzeys spoke about the use of phages as potential antibacterials and biotechnological applications. They noted that classic short-read RNA sequencing is difficult to interpret for phages. This is because short-read transcriptomes don’t distinguish between processed and primary transcripts. Putzeys focused on sequencing primary transcripts that have 5′ PPP caps. ONT-cappable-seq workflow starts by isolating RNA at different stages of phage infection. Libraries are prepared enriching for capped transcripts. The libraries were then sequenced on a PromethION. The resulting data are easier to interpret, identifying transcriptional starts and stops. Regions with high transcriptional activity are also easier to identify. With ONT-capped-seq, it is easier to study dense transcriptomes. I think their use of beads to capture 5′ PPP caps is very useful.
