Direct RNA nanopore sequencing of rRNA from mouse organs and cell lines.

RNA modifications are functional groups that decorate RNA molecules, changing their chemical and biological properties. It has been proposed that ribosome heterogeneity might stem from rRNA modifications, potentially leading to specialised functions. In this regard, previous studies have shown that some rRNA modifications are dynamically regulated during mammalian development; however, previous works were limited to the analysis of 2'O-methylated rRNA sites. Here, we employ direct RNA nanopore sequencing to study rRNA modification diversity and dynamics, for all RNA modification types present in rRNAs, across multiple mouse tissues and developmental stages. We find that several sites are dynamically modified during mammalian development and that some rRNA modifications are in fact tissue-specific, finding that the adult brain has the most distinct rRNA modification pattern from all the tissues and stages analysed. Moreover, we identify several unannotated rRNA modifications sites, some of which show dynamic modification patterns. Notably, we find that modification patterns do not correlate with expression levels of the rRNA modification enzymes, nor with snoRNA expression levels.