Abstract
Methyl-7-guanosine (m7G) “capping” of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E (eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and increased capping efficiency of ∼100 coding and noncoding RNAs. To quantify this, we developed enzymatic (cap quantification; CapQ) and quantitative cap immunoprecipitation (CapIP) methods. The CapQ method has the further advantage that it captures information about capping status independent of the type of 5′ cap, i.e., it is not restricted to informing on m7G caps. These methodological advances led to unanticipated revelations: 1) Many RNA populations are inefficiently capped at steady state (∼30 to 50%), and eIF4E overexpression increased this to ∼60 to 100%, depending on the RNA; 2) eIF4E physically associates with noncoding RNAs in the nucleus; and 3) approximately half of eIF4E-capping targets identified are noncoding RNAs. eIF4E’s association with noncoding RNAs strongly positions it to act beyond translation. Coding and noncoding capping targets have activities that influence survival, cell morphology, and cell-to-cell interaction. Given that RNA export and translation machineries typically utilize capped RNA substrates, capping regulation provides means to titrate the protein-coding capacity of the transcriptome and, for noncoding RNAs, to regulate their activities. We also discovered a cap sensitivity element (CapSE) which conferred eIF4E-dependent capping sensitivity. Finally, we observed elevated capping for specific RNAs in high-eIF4E leukemia specimens, supporting a role for cap dysregulation in malignancy. In all, levels of capping RNAs can be regulated by eIF4E.
Original language | English (US) |
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Pages (from-to) | 26773-26783 |
Number of pages | 11 |
Journal | Proceedings of the National Academy of Sciences of the United States of America |
Volume | 117 |
Issue number | 43 |
DOIs | |
State | Published - Oct 27 2020 |
Funding
ACKNOWLEDGMENTS. We are grateful for helpful discussions with Drs. Esterina D’Asti, Mehdi Ghram, and Gavin Morris. We thank Jennifer Huber and Raphaelle Lambert for help with RNA-seq experiments. K.L.B.B. acknowledges financial support from NIH R01 CA80728, NIH R01 CA98571, Canadian Institutes of Health Research PJT159785, Leukemia & Lymphoma Society USA Translational Research Program (LLS USA TRP) R6513-20, and the Canada Research Chair in Molecular Biology of the Cell Nucleus. L.C. acknowledges financial support from LLS USA TRP R6510-19 and M.V.R. acknowledges financial support from the Kellen Foundation and a Department of Medicine Postdoctoral Scholar Award. We are grateful for helpful discussions with Drs. Esterina D?Asti, Mehdi Ghram, and Gavin Morris. We thank Jennifer Huber and Raphaelle Lambert for help with RNA-seq experiments. K.L.B.B. acknowledges financial support from NIH R01 CA80728, NIH R01 CA98571, Canadian Institutes of Health Research PJT159785, Leukemia & Lymphoma Society USA Translational Research Program (LLS USA TRP) R6513-20, and the Canada Research Chair in Molecular Biology of the Cell Nucleus. L.C. acknowledges financial support from LLS USA TRP R6510-19 and M.V.R. acknowledges financial support from the Kellen Foundation and a Department of Medicine Postdoctoral Scholar Award.
Keywords
- EIF4E
- Methyl-7-guanosine cap
- RNA capping
- RNMT
ASJC Scopus subject areas
- General