Mulligan, M. J. et al. Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults. Nature 586, 589–593 (2020).
Morais, P., Adachi, H. & Yu, Y.-T. The critical contribution of pseudouridine to mRNA COVID-19 vaccines. Front. Cell Dev. Biol. 9, 789427 (2021).
Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022).
Jackson, R. J., Hellen, C. U. T. & Pestova, T. V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113–127 (2010).
von der Haar, T., Gross, J. D., Wagner, G. & McCarthy, J. E. G. The mRNA cap-binding protein eIF4E in post-transcriptional gene expression. Nat. Struct. Mol. Biol. 11, 503–511 (2004).
Despic, V. & Jaffrey, S. R. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature 614, 358–366 (2023).
Züst, R. et al. Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat. Immunol. 12, 137–143 (2011).
Ramanathan, A., Robb, G. B. & Chan, S.-H. mRNA capping: biological functions and applications. Nucleic Acids Res. 44, 7511–7526 (2016).
Grudzien‐Nogalska, E. et al. Synthesis of anti‐reverse cap analogs (ARCAs) and their applications in mRNA translation and stability. Methods Enzymol. 431, 203–227 (2007).
Stepinski, J., Waddell, C., Stolarski, R., Darzynkiewicz, E. & Rhoads, R. E. Synthesis and properties of mRNAs containing the novel ‘anti-reverse’ cap analogs 7-methyl(3′-O-methyl)GpppG and 7-methyl(3′-deoxy)GpppG. RNA 7, 1486–1495 (2001).
Ishikawa, M., Murai, R., Hagiwara, H., Hoshino, T. & Suyama, K. Preparation of eukaryotic mRNA having differently methylated adenosine at the 5′-terminus and the effect of the methyl group in translation. Nucleic Acids Symp. Ser. 53, 129–130 (2009).
Sikorski, P. J. et al. The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5′ cap modulates protein expression in living cells. Nucleic Acids Res. 48, 1607–1626 (2020).
Jurga, S. & Barciszewski, J. (eds) Messenger RNA Therapeutics (Springer Nature, 2022).
Wesselhoeft, R. A., Kowalski, P. S. & Anderson, D. G. Engineering circular RNA for potent and stable translation in eukaryotic cells. Nat. Commun. 9, 2629 (2018).
Chen, R. et al. Engineering circular RNA for enhanced protein production. Nat. Biotechnol. 41, 262–272 (2023).
Qu, L. et al. Circular RNA vaccines against SARS-CoV-2 and emerging variants. Cell 185, 1728–1744 (2022).
Koch, A., Aguilera, L., Morisaki, T., Munsky, B. & Stasevich, T. J. Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells. Nat. Struct. Mol. Biol. 27, 1095–1104 (2020).
Abe, N. et al. Complete chemical synthesis of minimal messenger RNA by efficient chemical capping reaction. ACS Chem. Biol. 17, 1308–1314 (2022).
Kawaguchi, D. et al. Phosphorothioate modification of mRNA accelerates the rate of translation initiation to provide more efficient protein synthesis. Angew. Chem. Int. Ed. Engl. 59, 17403–17407 (2020).
Wojcik, R. et al. Novel N7-arylmethyl substituted dinucleotide mRNA 5′ cap analogs: synthesis and evaluation as modulators of translation. Pharmaceutics 13, 1941 (2021).
Chen, X. et al. Structure-guided design, synthesis, and evaluation of guanine-derived inhibitors of the eIF4E mRNA–cap interaction. J. Med. Chem. 55, 3837–3851 (2012).
Inagaki, M. et al. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures. Nat. Commun. 14, 2657 (2023).
Kore, A. R., Shanmugasundaram, M., Charles, I., Vlassov, A. V. & Barta, T. J. Locked nucleic acid (LNA)-modified dinucleotide mRNA cap analogue: synthesis, enzymatic incorporation, and utilization. J. Am. Chem. Soc. 131, 6364–6365 (2009).
Senthilvelan, A. et al. Trinucleotide cap analogue bearing a locked nucleic acid moiety: synthesis, mRNA modification, and translation for therapeutic applications. Org. Lett. 23, 4133–4136 (2021).
Aitken, C. E. & Lorsch, J. R. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 19, 568–576 (2012).
Gu, Y., Mao, Y., Jia, L., Dong, L. & Qian, S.-B. Bi-directional ribosome scanning controls the stringency of start codon selection. Nat. Commun. 12, 6604 (2021).
Aditham, A. et al. Chemically modified mocRNAs for highly efficient protein expression in mammalian cells. ACS Chem. Biol. 17, 3352–3366 (2022).
Hellman, L. M. & Fried, M. G. Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions. Nat. Protoc. 2, 1849–1861 (2007).
Nagaraj, N. et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011).
Mitchell, S. F. et al. The 5′-7-methylguanosine cap on eukaryotic mRNAs serves both to stimulate canonical translation initiation and to block an alternative pathway. Mol. Cell 39, 950–962 (2010).
Balatsos, N. A. A., Maragozidis, P., Anastasakis, D. & Stathopoulos, C. Modulation of poly(A)-specific ribonuclease (PARN): current knowledge and perspectives. Curr. Med. Chem. 19, 4838–4849 (2012).
Gerbracht, J. V. et al. CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. Nucleic Acids Res. 48, 8626–8644 (2020).
Hu, W., Sweet, T. J., Chamnongpol, S., Baker, K. E. & Coller, J. Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225–229 (2009).
van Dijk, E. et al. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21, 6915–6924 (2002).
Wojtczak, B. A. et al. 5′-Phosphorothiolate dinucleotide cap analogues: reagents for messenger RNA modification and potent small-molecular inhibitors of decapping enzymes. J. Am. Chem. Soc. 140, 5987–5999 (2018).
Bohlen, J., Roiuk, M., Neff, M. & Teleman, A. A. PRRC2 proteins impact translation initiation by promoting leaky scanning. Nucleic Acids Res. 51, 3391–3409 (2023).
Garshott, D. M. et al. iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation. Cell Rep. 36, 109642 (2021).
Ostrowski, L. A., Hall, A. C. & Mekhail, K. Ataxin-2: from RNA control to human health and disease. Genes 8, 157 (2017).
Hildebrandt, A. et al. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol. 20, 216 (2019).
Pattabhi, S., Knoll, M. L., Gale, M. Jr & Loo, Y.-M. DHX15 is a coreceptor for RLR signaling that promotes antiviral defense against RNA virus infection. J. Interferon Cytokine Res. 39, 331–346 (2019).
Xing, J. et al. DHX15 is required to control RNA virus-induced intestinal inflammation. Cell Rep. 35, 109205 (2021).
Wang, Y. et al. Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I. Nat. Struct. Mol. Biol. 17, 781–787 (2010).
Wang, X. et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361, eaat5691 (2018).
Zeng, H. et al. Spatially resolved single-cell translatomics at molecular resolution. Science 380, eadd3067 (2023).
Chen, H. et al. Branched chemically modified poly(A) tails enhance the translation capacity of mRNA. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02174-7 (2024).
Lee, A. S., Kranzusch, P. J., Doudna, J. A. & Cate, J. H. D. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature 536, 96–99 (2016).
Moerke, N. J. et al. Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G. Cell 128, 257–267 (2007).
Wesselhoeft, R. A. et al. RNA circularization diminishes immunogenicity and can extend translation duration in vivo. Mol. Cell 74, 508–520 (2019).
Karikó, K. et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol. Ther. 16, 1833–1840 (2008).
Cervantes, J. L., Weinerman, B., Basole, C. & Salazar, J. C. TLR8: the forgotten relative revindicated. Cell. Mol. Immunol. 9, 434–438 (2012).
Rehwinkel, J. & Gack, M. U. RIG-I-like receptors: their regulation and roles in RNA sensing. Nat. Rev. Immunol. 20, 537–551 (2020).
Chen, Y. G. et al. N6-methyladenosine modification controls circular RNA immunity. Mol. Cell 76, 96–109 (2019).
Lee, Y., Choe, J., Park, O. H. & Kim, Y. K. Molecular mechanisms driving mRNA degradation by m6A modification. Trends Genet. 36, 177–188 (2020).
Jain, S. et al. Modulation of translational decoding by m6A modification of mRNA. Nat. Commun. 14, 4784 (2023).
Ehret, F., Zhou, C. Y., Alexander, S. C., Zhang, D. & Devaraj, N. K. Site-specific covalent conjugation of modified mRNA by tRNA guanine transglycosylase. Mol. Pharm. 15, 737–742 (2018).
Meyer, K. D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).
Kumar, P., Hellen, C. U. T. & Pestova, T. V. Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev. 30, 1573–1588 (2016).
Hellen, C. U. & Sarnow, P. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 15, 1593–1612 (2001).
Brito Querido, J. et al. Structure of a human 48S translational initiation complex. Science 369, 1220–1227 (2020).
Querido, J. B. et al. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat. Struct. Mol. Biol. 31, 455–464 (2024).
Kozak, M. Adherence to the first-AUG rule when a second AUG codon follows closely upon the first. Proc. Natl Acad. Sci. USA 92, 2662–2666 (1995).
Eschbach, J. W., Kelly, M. R., Haley, N. R., Abels, R. I. & Adamson, J. W. Treatment of the anemia of progressive renal failure with recombinant human erythropoietin. N. Engl. J. Med. 321, 158–163 (1989).
Karikó, K., Muramatsu, H., Keller, J. M. & Weissman, D. Increased erythropoiesis in mice injected with submicrogram quantities of pseudouridine-containing mRNA encoding erythropoietin. Mol. Ther. 20, 948–953 (2012).
Jang, D.-I. et al. The role of tumor necrosis factor alpha (TNF-α) in autoimmune disease and current TNF-α inhibitors in therapeutics. Int. J. Mol. Sci. 22, 2719 (2021).
Giannini, E. G., Testa, R. & Savarino, V. Liver enzyme alteration: a guide for clinicians. CMAJ 172, 367–379 (2005).
Liang, Q. et al. RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants. iScience 25, 104043 (2022).
Vogel, A. B. et al. BNT162b vaccines protect rhesus macaques from SARS-CoV-2. Nature 592, 283–289 (2021).
Maher, K. et al. Mitigating autocorrelation during spatially resolved transcriptomics data analysis. Preprint at bioRxiv https://doi.org/10.1101/2023.06.30.547258 (2023).
Cheng, Q. et al. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing. Nat. Nanotechnol. 15, 313–320 (2020).
Riol-Blanco, L. et al. The chemokine receptor CCR7 activates in dendritic cells two signaling modules that independently regulate chemotaxis and migratory speed. J. Immunol. 174, 4070–4080 (2005).
Johnson, A. M. et al. Cancer cell-intrinsic expression of MHC class II regulates the immune microenvironment and response to anti-PD-1 therapy in lung adenocarcinoma. J. Immunol. 204, 2295–2307 (2020).
Kratky, W., Reis e Sousa, C., Oxenius, A. & Spörri, R. Direct activation of antigen-presenting cells is required for CD8+ T-cell priming and tumor vaccination. Proc. Natl Acad. Sci. USA 108, 17414–17419 (2011).
Laczkó, D. et al. A single immunization with nucleoside-modified mRNA vaccines elicits strong cellular and humoral immune responses against SARS-CoV-2 in mice. Immunity 53, 724–732 (2020).
Calabro, S. et al. Differential intrasplenic migration of dendritic cell subsets tailors adaptive immunity. Cell Rep. 16, 2472–2485 (2016).
Dohnalkova, M. et al. Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility. Cell Rep. 42, 112786 (2023).
Haussmann, I. U. et al. CMTr cap-adjacent 2′-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses. Nat. Commun. 13, 1209 (2022).
Someya, T., Ando, A., Kimoto, M. & Hirao, I. Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry. Nucleic Acids Res. 43, 6665–6676 (2015).
Pellestor, F. & Paulasova, P. The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics. Eur. J. Hum. Genet. 12, 694–700 (2004).
Corey, D. R. & Abrams, J. M. Morpholino antisense oligonucleotides: tools for investigating vertebrate development. Genome Biol. 2, reviews1015.1–reviews1015.3 (2001).
Hewitt, S. L. et al. Durable anticancer immunity from intratumoral administration of IL-23, IL-36γ, and OX40L mRNAs. Sci. Transl. Med. 11, eaat9143 (2019).
Musunuru, K. et al. In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates. Nature 593, 429–434 (2021).
Arevalo, C. P. et al. A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes. Science 378, 899–904 (2022).
Foy, S. P. et al. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature 615, 687–696 (2023).
Granit, V. et al. Safety and clinical activity of autologous RNA chimeric antigen receptor T-cell therapy in myasthenia gravis (MG-001): a prospective, multicentre, open-label, non-randomised phase 1b/2a study. Lancet Neurol. 22, 578–590 (2023).
Cai, A. et al. Quantitative assessment of mRNA cap analogues as inhibitors of in vitro translation. Biochemistry 38, 8538–8547 (1999).
Flamme, M., McKenzie, L. K., Sarac, I. & Hollenstein, M. Chemical methods for the modification of RNA. Methods 161, 64–82 (2019).
Zhang, X. et al. Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates. Proc. Natl Acad. Sci. USA 116, 2919–2924 (2019).
Shi, H. et al. Spatial atlas of the mouse central nervous system at molecular resolution. Nature 622, 552–561 (2023).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Weigert, M., Schmidt, U., Haase, R., Sugawara, K. & Myers, G. Star-convex polyhedra for 3D object detection and segmentation in microscopy. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (eds Ross, A., Cox, D. & McCloskey, S.) 3666–3673 (IEEE, 2020).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007).
Edupuganti, R. R. et al. N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat. Struct. Mol. Biol. 24, 870–878 (2017).
Alexander, S. C., Busby, K. N., Cole, C. M., Zhou, C. Y. & Devaraj, N. K. Site-specific covalent labeling of RNA by enzymatic transglycosylation. J. Am. Chem. Soc. 137, 12756–12759 (2015).
Meier, S., Güthe, S., Kiefhaber, T. & Grzesiek, S. Foldon, the natural trimerization domain of T4 fibritin, dissociates into a monomeric A-state form containing a stable β-hairpin: atomic details of trimer dissociation and local β-hairpin stability from residual dipolar couplings. J. Mol. Biol. 344, 1051–1069 (2004).
Chen, H. et al. Raw SILAC mass spectrometry data of chemical and topological design of multi-capped mRNA and capped circular RNA. Zenodo https://doi.org/10.5281/zenodo.12611469 (2024).
Chen, H. et al. Lymph node STARmap/RIBOmap dataset of chemical and topological design of multi-capped mRNA and capped circular RNA. Zenodo https://doi.org/10.5281/zenodo.12518588 (2024).
Source link
Leave a Comment