Tinoco, I. Jr & Bustamante, C. How RNA folds. J. Mol. Biol. 293, 271–281 (1999).
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). A comprehensive review that covers how the structural dynamics of RNA control cellular functions.
Al-Hashimi, H. M. & Walter, N. G. RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321–329 (2008).
Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002).
Mironov, A. S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002).
Batey, R. T., Gilbert, S. D. & Montange, R. K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004).
Flores, J. K. & Ataide, S. F. Structural changes of RNA in complex with proteins in the SRP. Front. Mol. Biosci. 5, 7 (2018).
Shi, H. et al. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat. Commun. 11, 5531 (2020).
Vicens, Q. & Kieft, J. S. Thoughts on how to think (and talk) about RNA structure. Proc. Natl Acad. Sci. USA 119, e2112677119 (2022).
Westhof, E. & Patel, D. J. Nucleic acids. From self-assembly to induced-fit recognition. Curr. Opin. Struct. Biol. 7, 305–309 (1997).
Sussman, J. L., Holbrook, S. R., Warrant, R. W., Church, G. M. & Kim, S. H. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J. Mol. Biol. 123, 607–630 (1978).
Fürtig, B., Richter, C., Wöhnert, J. & Schwalbe, H. NMR spectroscopy of RNA. Chembiochem 4, 936–962 (2003).
Leontis, N. B. & Zirbel, C. L. in RNA 3D Structure Analysis and Prediction (eds Leontis, N. & Westhof, E.) 281–298 (Springer Berlin Heidelberg, 2012).
Holley, R. W. et al. Structure of a ribonucleic acid. Science 147, 1462–1465 (1965).
Peattie, D. A. & Gilbert, W. Chemical probes for higher-order structure in RNA. Proc. Natl Acad. Sci. USA 77, 4679–4682 (1980).
Wang, X. D. & Padgett, R. A. Hydroxyl radical ‘footprinting’ of RNA: application to pre-mRNA splicing complexes. Proc. Natl Acad. Sci. USA 86, 7795–7799 (1989).
Latham, J. A. & Cech, T. R. Defining the inside and outside of a catalytic RNA molecule. Science 245, 276–282 (1989).
Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J. S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014).
Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75–82 (2017).
Smola, M. J., Rice, G. M., Busan, S., Siegfried, N. A. & Weeks, K. M. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat. Protoc. 10, 1643–1669 (2015).
Van Damme, R. et al. Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat. Commun. 13, 911 (2022).
Hafner, M. et al. CLIP and complementary methods. Nat. Rev. Methods Prim. 1, 1–23 (2021).
Weidmann, C. A., Mustoe, A. M., Jariwala, P. B., Calabrese, J. M. & Weeks, K. M. Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA. Nat. Biotechnol. 39, 347–356 (2020).
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).
Spitale, R. C. & Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. https://doi.org/10.1038/s41576-022-00546-w (2022).
Nutiu, R. et al. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol. 29, 659–664 (2011). This paper reports the first implementation of a high-throughput biophysical measurement on a sequencing chip, involving binding of the yeast transcription factor GCn4 to a library of DNA sites.
Tome, J. M. et al. Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. Nat. Methods 11, 683–688 (2014). This paper reports one of the first implementations of high-throughput biophysical measurements on sequencing chips for RNA, involving the binding of GFP and NELF-E to RNA aptamers.
Buenrostro, J. D. et al. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat. Biotechnol. 32, 562–568 (2014). This paper reports one of the first implementations of high-throughput biophysical measurements on sequencing chips for RNA, involving binding of the coat protein of MS2 bacteriophage to RNA hairpins.
Layton, C. J., McMahon, P. L. & Greenleaf, W. J. Large-scale, quantitative protein assays on a high-throughput DNA sequencing chip. Mol. Cell 73, 1075–1082.e4 (2019).
Yesselman, J. D. et al. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proc. Natl Acad. Sci. USA 116, 16847–16855 (2019). In this paper, the authors study RNA–RNA binding using tectoRNAs on the RNA array and construct a structure-based model that can predict experimental binding energies.
She, R. et al. Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome. Proc. Natl Acad. Sci. USA 114, 3619–3624 (2017).
Li, Z. et al. DNB-based on-chip motif finding: a high-throughput method to profile different types of protein-DNA interactions. Sci. Adv. 6, eabb3350 (2020).
Ozer, A. et al. Quantitative assessment of RNA-protein interactions with high-throughput sequencing–RNA affinity profiling. Nat. Protoc. 10, 1212–1233 (2015).
Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H. & Bartel, D. P. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66–71 (2014).
Denny, S. K. et al. High-throughput investigation of diverse junction elements in RNA tertiary folding. Cell 174, 377–390.e20 (2018).
Jarmoskaite, I. et al. A quantitative and predictive model for RNA binding by human Pumilio proteins. Mol. Cell 74, 966–981.e18 (2019).
Wu, M. J., Andreasson, J. O. L., Kladwang, W., Greenleaf, W. & Das, R. Automated design of diverse stand-alone riboswitches. ACS Synth. Biol. 8, 1838–1846 (2019).
Becker, W. R. et al. High-throughput analysis reveals rules for target RNA binding and cleavage by AGO2. Mol. Cell 75, 741–755.e11 (2019).
Becker, W. R. et al. Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding. Preprint at bioRxiv https://doi.org/10.1101/571588 (2019).
Andreasson, J. O. L., Savinov, A., Block, S. M. & Greenleaf, W. J. Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme. Nat. Commun. 11, 1663 (2020).
Bonilla, S. L. et al. High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs. Proc. Natl Acad. Sci. USA 118, e2109085118 (2021).
Andreasson, J. O. L. et al. Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. Proc. Natl Acad. Sci. USA 119, e2112979119 (2022).
Jung, C. et al. Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips. Cell 170, 35–47.e13 (2017).
Jones, S. K. Jr et al. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat. Biotechnol. 39, 84–93 (2021).
Denny, S. K. & Greenleaf, W. J. Linking RNA sequence, structure, and function on massively parallel high-throughput sequencers. Cold Spring Harb. Perspect. Biol. 11, a032300 (2019).
Bartel, D. P. Metazoan microRNAs. Cell 173, 20–51 (2018).
Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).
Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 (1996).
留言 (0)