Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes

Abstract

Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (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 displays 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 in human cells. Using RiboMethSeq, a nonbiased 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 internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.

METTL5, an 18S rRNA-specific m6A methyltransferase, modulates expression of stress response genes

“…Akin to METTL5, loss of the large subunit ribosomal protein Rpl38 doesn't affect global protein synthesis, but perturbs translation of a select subset of Hox mRNAs (43). Additionally, a repertoire of 2′-O-methylation sites in rRNA were identified to be subjected to variations and it was demonstrated that functional domains of ribosomes are targets of 2′-O-methylation plasticity (44). Moreover, the 28S rRNA A4220 is not always 100% methylated, e.g., it is about 50% level in HepG2 cells (9), suggesting that HepG2 cells may have ribosomes with and without m 6 A4220.…”

The role of genomic vs. epigenomic variation in shaping patterns of convergent transcriptomic variation across continents in a young species complex

“…Such mechanism within the ribosome is particularly important in the regulation of the gene expression [58]. Moreover, some functional domains of ribosomes have been shown to be targeted by the rRNA2'-O-me, inducing a modulation of the translation of mRNAs through plastic response [59]. Thus, such mechanisms suggest an indirect gene expression regulation through DNA methylation.…”

A novel platform of RNA 2′-O-methylation high-throughput and site-specific quantification tools revealed its broad distribution on mRNA

“…The entire function of 2'-O-methylation remained unclear, which was limited to a research tool. The previous study suggested that Nm seemed to involved in immune response via mRNA 5' cap Nm sites, mRNA alternative splicing mediated by intron branch point, maintaining the secondary structure of rRNA, and regulating protein translation by interfering tRNA-mRNA or mRNA-rRNA interactions [5,6,11,14,21]. Based on our preliminary data shown in this article, the roles of Nm sites in cells were much more prevalent than we expected.…”

“…In the past few years, three high throughput Nm detection methods had been developed, which were 2'OMe-seq [12,13], RiboMethSeq [14][15][16] and Nm-seq [7]. The principle of 2'OMe-seq was based on the block of RNA reverse transcription at a low concentration of dNTPs.…”