Bernardo Aguzzoli Heberle from the University of Kentucky presented at London Calling 2023 on “Oxford Nanopore long-read RNA sequencing enables precise RNA isoform discovery and quantification in human brains.” They shared an example of how longer reads allow for better RNA isoform quantification and discovery. Aguzzoli Heberle also noted that Nanopore sequencing yields more uniquely aligned reads. There is also a tradeoff between direct RNA sequencing and amplification of cDNA methods: direct RNA reads provide better alignment but lower throughput. For their method they took twelve aged human brain samples (six female and six female) and did PCR cDNA library prep. They sequenced on one PromethION flow cell per sample. The team used Bambu for quantification and analysis. The research uncovered 428 new transcripts!Several new transcripts in frontal context tissue were from 49 medically-relevant genes. TREM2 novel isoforms were identified including one that was studied by a lab down the hall and on Aguzzoli Heberle’s dissertation committee! Their results closely agreed. RNA that was discovered from unannotated regions of the genome was found. The team discovered 267 “new gene bodies” with this approach. Aguzzoli Heberle did achieve their goal of emphasizing how long-read approaches provide a new and powerful tool to identify novel isoforms and genes. In their studies, Aguzzoli Heberle found new regions of gene expression and isoforms relevant in aging. My goal is to figure out how to reliably and efficiently conduct direct RNA sequencing and transcriptomics for Delftia acidovorans and other organisms.
