FBL catalyzes internal 2′-O-Methylation in mRNA to promote RNA stability

2′-O-Methylation is prominent in ribosome RNA catalyzed by Fibrillarin (FBL). However, the stoichiometry of 2′-O-methylation at base resolution in the internal mRNA and its functions remain to be explored. Here, we firstly investigate the effect of the 2′-O-methylation on the mRNA stability and expression at a genome-wide scale. Combined with Nanopore sequencing and a machine learning strategy, we identified thousands of RNA methylation sites in mRNA and rRNA at base resolution. The mRNA half-life profiling of FBL deficient cells established a direct effect of RNA methylation and FBL binding on the mRNA stability. We further determined the RNA methylation on the expression levels and tested the post-transcriptional effect of elevated FBL mediated 2′-O-Methylation in mRNA within the prostate cancer model. Besides the role of the translational regulation of FBL in rRNA, elevated FBL promotes cancer progress by stabilizing the mRNA through RNA binding and 2′-O-Methylation. Our results reveal a novel mechanism that FBL regulates the 2′-O-methylation and turnover of mRNA at whole transcriptome levels. Examination of mRNA half-life, in replicative analysis with NGS RNA-seq, with 2 replicates at siCTRL, siFBL and shNOP56 at time point 0h, 6h, 12h, 24h for HEK293T cells. Examination of mRNA half-life, in replicative analysis with NGS RNA-seq, with 2 replicates at siCTRL, siFBL in C4-2 cell line at 0h, 3h, 6h, 12h. Nanopore directive RNA-seq for the RNA modification detection for siCTRL and siFBL were performed with two replicates. Examination of mRNA half-life, in replicative analysis with SLAM-seq RNA-seq, with 2 replicates at siCTRL, siFBL in C4-2 cell line at 0h, 6h,12h,24h.