biostudies-literatureLi YNHLBI NIH HHSNCI NIH HHSNIGMS NIH HHSNIH HHS2320-2336.e6https://www.ebi.ac.uk/biostudies/studies/S-EPMC11196006biostudies-literatureUnknown84(12)2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.Molecular cell2'-O-methylation at internal sites on mRNA promotes mRNA stability.PMC11196006R01 HL155632P50 CA180995S10 OD025194R01 GM138407R01 HL133254S10 OD025120R01 CA278832R01 HL148338R01 CA256741P30 CA060553P41 GM108569R01 GM125632R01 CA208257Gao BLi YYi YChen KWang RZhang YGao XWang XZhao DZhang LZhang LSCao Qfalse2'-O-methylation at internal sites on mRNA promotes mRNA stability.2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.2024-01-01T00:00:00Z2024 Jun2026-06-02T01:13:57.021Z2026-05-24T03:07:53.329ZS-EPMC111960063890611510.1016/j.molcel.2024.04.011