Logan Mulroney from the EMBL-EBI & Center for Genomic Science at the Italian Institute of Technology in Italy presented at London Calling 2024 “A survey of human RNA modifications by direct RNA nanopore sequencing.” Mulroney described RNA modifications as “chemical alterations to canonical nucleotides” and mentioned that they have been implicated in diseases such as cancer. Mulroney noted that there are ~170 known naturally occurring RNA modifications. These modifications have been primarily detected by mass spectrometry or short-read assays. With direct RNA sequencing and Nanopore devices, RNA modifications can be detected. However, this is a comparative method: you must have a reference signal from a known modification. Mulroney explained that their method creates IVT RNA from a transcriptome of interest. Mulroney isolated RNA from a cell line of interest (K562) in two native conditions and two in vitro transcribed (IVT). They found motifs associated with m6A and m5C are enriched in significant sites. Mulroney shared an example of a putative m5C found in proximity to putative m6A in cancer-associated BCR. Interestingly, modifications seem to be deposited randomly. Mulroney concluded that the IVT reference is useful for simultaneously detecting multiple RNA modifications from the same sample, but the analysis is challenging. There also appears to be a “consistent pattern of m5C sites associated with m6A sites.” I find the RNA modification field intriguing and enjoy learning about the approaches used.
