Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing

RNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C, m7G and ? modification. Finally, we illustrated a global view of epitranscriptome with m6A, m1A, m5C, m7G and ? modification in rice seedlings under normal and high salinity environment. In summary, we provided a strategy for creating IVET resource from cDNA library and developed a computational method that use IVET-based transfer learning termed TandemMod for profiling epitranscriptome landscape with co-occupancy of multiple types of RNA modification in plants responsive to environmental signal. Overall design: Comparative epitranscriptome profiling analysis of DRS data for rice seedings under normal and high salinity environment.