For instance, N 1-methyladenosine (m 1A) can block the Watson-Crick interface and is vital for tRNA stability and the replication of HIV-1. Besides m 6A, there are also a number of RNA modifications with crucial biological functions. It also plays various roles in disease pathogenesis such as carcinoma, breast tumor, gastric cancer, and anti-tumor immunity. It is involved in many biological processes such as the circadian clock, differentiation from naïve pluripotency, and the heat shock response. M 6A occurs on nascent pre-mRNA, regulating its stability and translation. More than 100 different types of RNA modifications have been identified 2, and among them, N 6-methyladenosine (m 6A) is the most common eukaryotic mRNA modification. Precise identification of RNA modification sites is therefore of crucial importance to understanding the functions and regulatory mechanisms of various RNAs. Post-transcriptional RNA modifications increase the structural and functional diversity of RNA molecules and regulate all stages of RNA life 1. Our work provides a solution for detecting multiple RNA modifications, enabling an integrated analysis of these RNA modifications, and gaining a better understanding of sequence-based RNA modification mechanisms. Importantly, our model revealed a strong association among different types of RNA modifications from the perspective of their associated sequence contexts. Built upon an attention-based multi-label deep learning framework, MultiRM not only simultaneously predicts the putative sites of twelve widely occurring transcriptome modifications (m 6A, m 1A, m 5C, m 5U, m 6Am, m 7G, Ψ, I, Am, Cm, Gm, and Um), but also returns the key sequence contents that contribute most to the positive predictions. Here, we present MultiRM, a method for the integrated prediction and interpretation of post-transcriptional RNA modifications from RNA sequences. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of RNAs. Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types.
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