Evidence for rRNA 2''-O-methylation plasticity: control of intrinsic translational capabilities of human ribosomes

Ribosomal RNAs (rRNAs) are main effectors of mRNA decoding, peptide-bond formation and ribosome dynamics during translation. Ribose 2''-O-methylation (2''-O-Me) is the most abundant rRNA chemical modification, and display a complex pattern in rRNA. 2''-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2''-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2''-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin (FBL) in human cells. Using RiboMethSeq, a non-biased quantitative mapping of 2''-O-Me, we identified a repertoire of 2''-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2''-O-Me plasticity. Using the cricket paralysis virus (CrPV) IRES element, as a model, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through 2''-O-Me pattern and not by non-ribosomal actors of the translational machinery. Our results establish rRNA 2''-O-methylation plasticity as a mechanism providing functional specificity to human ribosomes. Overall design: RNAseq was conducted to get the landscape of transcripts abundances. RIBOseq was conducted to observe the ribosome occupancy on each protein-coding gene of the hg38 genome assembly.