Leppek, K., Das, R. & Barna, M. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat. Rev. Mol. Cell Biol. 19, 158–174 (2018).
Mayr, C. Regulation by 3′-untranslated regions. Annu. Rev. Genet. 51, 171–194 (2017).
Frankish, A. et al. GENCODE 2021. Nucleic Acids Res. 49, D916–D923 (2021).
Fu, X.-D. Non-coding RNA: a new frontier in regulatory biology. Natl Sci. Rev. 1, 190–204 (2014).
Mustoe, A. M., Brooks, C. L. & Al-Hashimi, H. M. Hierarchy of RNA functional dynamics. Annu. Rev. Biochem. 83, 441–466 (2014).
CAS PubMed PubMed Central Google Scholar
Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019).
CAS PubMed PubMed Central Google Scholar
Kortmann, J. & Narberhaus, F. Bacterial RNA thermometers: molecular zippers and switches. Nat. Rev. Microbiol. 10, 255–265 (2012).
Serganov, A. & Nudler, E. A decade of riboswitches. Cell 152, 17–24 (2013).
CAS PubMed PubMed Central Google Scholar
Kubota, M., Tran, C. & Spitale, R. C. Progress and challenges for chemical probing of RNA structure inside living cells. Nat. Chem. Biol. 11, 933–941 (2015).
CAS PubMed PubMed Central Google Scholar
Strobel, E. J., Yu, A. M. & Lucks, J. B. High-throughput determination of RNA structures. Nat. Rev. Genet. 19, 615–634 (2018).
CAS PubMed PubMed Central Google Scholar
Kwok, C. K., Tang, Y., Assmann, S. M. & Bevilacqua, P. C. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem. Sci. 40, 221–232 (2015).
Wells, S. E., Hughes, J. M., Igel, A. H. & Ares, M. Use of dimethyl sulfate to probe RNA structure in vivo. Methods Enzymol. 318, 479–493 (2000).
Mustoe, A. M., Lama, N. N., Irving, P. S., Olson, S. W. & Weeks, K. M. RNA base-pairing complexity in living cells visualized by correlated chemical probing. Proc. Natl Acad. Sci. USA 116, 24574–24582 (2019).
CAS PubMed PubMed Central Google Scholar
Mitchell, D. et al. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 24, 114–124 (2018).
CAS PubMed PubMed Central Google Scholar
Wang, P. Y., Sexton, A. N., Culligan, W. J. & Simon, M. D. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 25, 135–146 (2019).
CAS PubMed PubMed Central Google Scholar
Mitchell, D. et al. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA 25, 147–157 (2019).
CAS PubMed PubMed Central Google Scholar
Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223–4231 (2005).
McGinnis, J. L., Dunkle, J. A., Cate, J. H. D. & Weeks, K. M. The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617–6624 (2012).
CAS PubMed PubMed Central Google Scholar
Xiao, L., Fang, L. & Kool, E. T. Acylation probing of “generic” RNA libraries reveals critical influence of loop constraints on reactivity. Cell Chem. Biol. 29, 1341–1352.e8 (2022).
Steen, K.-A., Rice, G. M. & Weeks, K. M. Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J. Am. Chem. Soc. 134, 13160–13163 (2012).
CAS PubMed PubMed Central Google Scholar
Mortimer, S. A. & Weeks, K. M. Time-resolved RNA SHAPE chemistry. J. Am. Chem. Soc. 130, 16178–16180 (2008).
Busan, S., Weidmann, C. A., Sengupta, A. & Weeks, K. M. Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry 58, 2655–2664 (2019).
Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18–20 (2013).
Spitale, R. C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).
CAS PubMed PubMed Central Google Scholar
Marinus, T., Fessler, A. B., Ogle, C. A. & Incarnato, D. A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy. Nucleic Acids Res. 49, e34 (2021).
CAS PubMed PubMed Central Google Scholar
Ingle, S., Azad, R. N., Jain, S. S. & Tullius, T. D. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res. 42, 12758–12767 (2014).
CAS PubMed PubMed Central Google Scholar
Kielpinski, L. J. & Vinther, J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res. 42, e70 (2014).
CAS PubMed PubMed Central Google Scholar
Feng, C. et al. Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nat. Chem. Biol. 14, 276–283 (2018).
CAS PubMed PubMed Central Google Scholar
Zinshteyn, B. et al. Assaying RNA structure with LASER-Seq. Nucleic Acids Res. 47, 43–55 (2019).
Homan, P. J. et al. Single-molecule correlated chemical probing of RNA. Proc. Natl Acad. Sci. USA 111, 13858–13863 (2014).
CAS PubMed PubMed Central Google Scholar
Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E. & Weeks, K. M. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods 11, 959–965 (2014).
CAS PubMed PubMed Central Google Scholar
Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75–82 (2017).
Guo, L.-T. et al. Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase. J. Mol. Biol. 432, 3338–3352 (2020).
CAS PubMed PubMed Central Google Scholar
Cimino, G. D., Gamper, H. B., Isaacs, S. T. & Hearst, J. E. Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Annu. Rev. Biochem. 54, 1151–1193 (1985).
Nilsen, T. W. Detecting RNA-RNA interactions using psoralen derivatives. Cold Spring Harb. Protoc. 2014, 996–1000 (2014).
Ramani, V., Qiu, R. & Shendure, J. High-throughput determination of RNA structure by proximity ligation. Nat. Biotechnol. 33, 980–984 (2015).
CAS PubMed PubMed Central Google Scholar
Lu, Z. et al. RNA duplex map in living cells reveals higher order transcriptome structure. Cell 165, 1267–1279 (2016).
CAS PubMed PubMed Central Google Scholar
Aw, J. G. A. et al. In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Mol. Cell 62, 603–617 (2016).
Sharma, E., Sterne-Weiler, T., O’Hanlon, D. & Blencowe, B. J. Global mapping of human RNA–RNA interactions. Mol. Cell 62, 618–626 (2016).
Nguyen, T. C. et al. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO. Nat. Commun. 7, 12023 (2016).
CAS PubMed PubMed Central Google Scholar
Ziv, O. et al. COMRADES determines in vivo RNA structures and interactions. Nat. Methods 15, 785–788 (2018).
CAS PubMed PubMed Central Google Scholar
Velema, W. A., Park, H. S., Kadina, A., Orbai, L. & Kool, E. T. Trapping transient RNA complexes by chemically reversible acylation. Angew. Chem. Int. Ed. Engl. 59, 22017–22022 (2020).
CAS PubMed PubMed Central Google Scholar
Van Damme, R. et al. Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat. Commun. 13
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