Adilakshmi,, T., Lease,, R. A., & Woodson,, S. A. (2006). Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation. Nucleic Acids Research, 34(8), e64. https://doi.org/10.1093/nar/gkl291
Adilakshmi,, T., Soper,, S. F. C., & Woodson,, S. A. (2009). Structural analysis of RNA in living cells by in vivo synchrotron X‐ray footprinting. Methods in Enzymology, 468(09), 239–258. https://doi.org/10.1016/S0076-6879(09)68012-5
Aird,, D., Ross,, M. G., Chen,, W.‐S., Danielsson,, M., Fennell,, T., Russ,, C., … Gnirke,, A. (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology, 12(2), R18. https://doi.org/10.1186/gb-2011-12-2-r18
Amunts,, A., Brown,, A., Bai,, X., Llácer,, J. L., Hussain,, T., Emsley,, P., … Ramakrishnan,, V. (2014). Structure of the yeast mitochondrial large ribosomal subunit. Science, 343(6178), 1485–1489. https://doi.org/10.1126/science.1249410
Anderson,, J. W. J., Haas,, P. A., Mathieson,, L.‐A., Volynkin,, V., Lyngsø,, R., Tataru,, P., & Hein,, J. (2013). Oxfold: Kinetic folding of RNA using stochastic context‐free grammars and evolutionary information. Bioinformatics, 29(6), 704–710. https://doi.org/10.1093/bioinformatics/btt050
Aviran,, S., Trapnell,, C., Lucks,, J. B., Mortimer,, S. A., Luo,, S., Schroth,, G. P., … Pachter,, L. (2011). Modeling and automation of sequencing‐based characterization of RNA structure. Proceedings of the National Academy of Sciences of the USA, 108(27), 11069–11074. https://doi.org/10.1073/pnas.1106541108
Aw,, J. G. A., Shen,, Y., Wilm,, A., Sun,, M., Lim,, X. N., Boon,, K.‐L., … Wan,, Y. (2016). In vivo mapping of eukaryotic RNA interactomes reveals principles of higher‐order organization and regulation. Molecular Cell, 62(4), 603–617. https://doi.org/10.1016/j.molcel.2016.04.028
Baudin,, F., Mougel,, M., Romby,, P., Eyermann,, F., Ebel,, J. P., Ehresmann,, B., & Ehresmann,, C. (1989). Probing the phosphates of the Escherichia coli ribosomal 16S RNA in its naked form, in the 30S subunit, and in the 70S ribosome. Biochemistry, 28(14), 5847–5855.
Benjamini,, Y., & Speed,, T. P. (2012). Summarizing and correcting the GC content bias in high‐throughput sequencing. Nucleic Acids Research, 40(10), e72. https://doi.org/10.1093/nar/gks001
Bevilacqua,, P. C., Ritchey,, L. E., Su,, Z., & Assmann,, S. M. (2016). Genome‐wide analysis of RNA secondary structure. Annual Review of Genetics, 50, 235–266. https://doi.org/10.1146/annurev-genet-120215-035034
Brunel,, C., Romby,, P., Westhof,, E., Ehresmann,, C., & Ehresmann,, B. (1991). Three‐dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. Journal of Molecular Biology, 221(1), 293–308.
Burlacu,, E., Lackmann,, F., Aguilar,, L.‐C., Belikov,, S., Nues,, R., Trahan,, C., … Granneman,, S. (2017). High‐throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast. Nature Communications, 8(1), 714. https://doi.org/10.1038/s41467-017-00761-8
Busan,, S., & Weeks,, K. M. (2017). Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA, 23(7), 1012–1018. https://doi.org/10.1261/rna.061945.117
Cantara,, W. A., Hatterschide,, J., Wu,, W., & Musier‐Forsyth,, K. (2017). RiboCAT: A new capillary electrophoresis data analysis tool for nucleic acid probing. RNA, 23(2), 240–249. https://doi.org/10.1261/rna.058404.116
Chan,, D., Beasley,, S., Zhen,, Y., & Spitale,, R. C. (2018). Facile synthesis and evaluation of a dual‐functioning furoyl probe for in‐cell SHAPE. Bioorganic %26 Medicinal Chemistry Letters, 28, 601–605. https://doi.org/10.1016/j.bmcl.2018.01.042
Chea,, E. E., & Jones,, L. M. (2018). Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting. The Analyst, 143(4), 798–807. https://doi.org/10.1039/c7an01323j
Cheng,, C. Y., Chou,, F.‐C., Kladwang,, W., Tian,, S., Cordero,, P., & Das,, R. (2015). Consistent global structures of complex RNA states through multidimensional chemical mapping. eLife, 4, e07600. https://doi.org/10.7554/eLife07600
Choudhary,, K., Ruan,, L., Deng,, F., Shih,, N., & Aviran,, S. (2017). SEQualyzer: Interactive tool for quality control and exploratory analysis of high‐throughput RNA structural profiling data. Bioinformatics, 33(3), 441–443. https://doi.org/10.1093/bioinformatics/btw627
Ciesiołka,, J., Michałowski,, D., Wrzesinski,, J., Krajewski,, J., & Krzyzosiak,, W. J. (1998). Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs. Journal of Molecular Biology, 275(2), 211–220. https://doi.org/10.1006/jmbi.1997.1462
Clementi,, N., Chirkova,, A., Puffer,, B., Micura,, R., & Polacek,, N. (2010). Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF‐G GTPase activation. Nature Chemical Biology, 6(5), 344–351. https://doi.org/10.1038/nchembio.341
Cordero,, P., & Das,, R. (2015). Rich RNA structure landscapes revealed by mutate‐and‐map analysis. PLoS Computational Biology, 11(11), e1004473. https://doi.org/10.1371/journal.pcbi.1004473
Cordero,, P., Kladwang,, W., Vanlang,, C. C., & Das,, R. (2012). Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry, 51(36), 7037–7039. https://doi.org/10.1021/bi3008802
Cruz,, J. A., & Westhof,, E. (2009). The dynamic landscapes of RNA architecture. Cell, 136(4), 604–609. https://doi.org/10.1016/j.cell.2009.02.003
Das,, R., Kudaravalli,, M., Jonikas,, M., Laederach,, A., Fong,, R., Schwans,, J. P., … Herschlag,, D. (2008). Structural inference of native and partially folded RNA by high‐throughput contact mapping. Proceedings of the National Academy of Sciences of the USA, 105(11), 4144–4149. https://doi.org/10.1073/pnas.0709032105
Das,, R., Laederach,, A., Pearlman,, S. M., Herschlag,, D., & Altman,, R. B. (2005). SAFA: Semi‐automated footprinting analysis software for high‐throughput quantification of nucleic acid footprinting experiments. RNA, 11(3), 344–354. https://doi.org/10.1261/rna.7214405
Deigan,, K. E., Li,, T. W., Mathews,, D. H., & Weeks,, K. M. (2009). Accurate SHAPE‐directed RNA structure determination. Proceedings of the National Academy of Sciences of the USA, 106(1), 97–102. https://doi.org/10.1073/pnas.0806929106
Ding,, Y., Kwok,, C. K., Tang,, Y., Bevilacqua,, P. C., & Assmann,, S. M. (2015). Genome‐wide profiling of in vivo RNA structure at single‐nucleotide resolution using structure‐seq. Nature Protocols, 10(7), 1050–1066. https://doi.org/10.1038/nprot.2015.064
Ding,, Y., Tang,, Y., Kwok,, C. K., Zhang,, Y., Bevilacqua,, P. C., & Assmann,, S. M. (2014). In vivo genome‐wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505(7485), 696–700. https://doi.org/10.1038/nature12756
Doniach,, S., & Lipfert,, J. (2009). Use of small angle X‐ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods in Enzymology, 469, 237–251. https://doi.org/10.1016/S0076-6879(09)69011-X
Dutca,, L. M., Gallagher,, J. E. G., & Baserga,, S. J. (2011). The initial U3 snoRNA:pre‐rRNA base pairing interaction required for pre‐18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39(12), 5164–5180. https://doi.org/10.1093/nar/gkr044
Eddy,, S. (2014). Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. Annual Review of Biophysics, 43, 433–456.
Ehresmann,, C., Baudin,, F., Mougel,, M., Romby,, P., Ebel,, J. P., & Ehresmann,, B. (1987). Probing the structure of RNAs in solution. Nucleic Acids Research, 15(22), 9109–9128.
Ennifar,, E., Walter,, P., Ehresmann,, B., Ehresmann,, C., & Dumas,, P. (2001). Crystal structures of coaxially stacked kissing complexes of the HIV‐1 RNA dimerization initiation site. Nature Structural Biology, 8(12), 1064–1068. https://doi.org/10.1038/nsb727
Enyeart,, P. J., Mohr,, G., Ellington,, A. D., & Lambowitz,, A. M. (2014). Biotechnological applications of mobile group II introns and their reverse transcriptases: Gene targeting, RNA‐seq, and non‐coding RNA analysis. Mobile DNA, 5, 2.
Fang,, X., Stagno,, J. R., Bhandari,, Y. R., Zuo,, X., & Wang,, Y.‐X. (2015). Small‐angle X‐ray scattering: A bridge between RNA secondary structures and three‐dimensional topological structures. Current Opinion in Structural Biology, 30, 147–160. https://doi.org/10.1016/j.sbi.2015.02.010
Feng,, C., Chan,, D., Joseph,, J., Muuronen,, M., Coldren,, W. H., Dai,, N., … Spitale,, R. C. (2018). Light‐activated chemical probing of nucleobase solvent accessibility inside cells. Nature Chemical Biology, 14(3), 276–283. https://doi.org/10.1038/nchembio.2548
Forconi,, M., & Herschlag,, D. (2009). Metal ion‐based RNA cleavage as a structural probe. Methods in Enzymology, 468, 91–106. https://doi.org/10.1016/S0076-6879(09)68005-8
Fuchs,, R. T., Sun,, Z., Zhuang,, F., & Robb,, G. B. (2015). Bias in ligation‐based small RNA sequencing library construction is determined by adaptor and RNA structure. PLoS One, 10(5), e0126049. https://doi.org/10.1371/journal.pone.0126049
Garneau,, N. L., Wilusz,, J., & Wilusz,, C. J. (2007). The highways and byways of mRNA decay. Nature Reviews Molecular Cell Biology, 8(2), 113–126. https://doi.org/10.1038/nrm2104
Gherghe,, C. M., Mortimer,, S. A., Krahn,, J. M., Thompson,, N. L., & Weeks,, K. M. (2008). Slow conformational dynamics at C2′‐endo nucleotides in RNA. Journal of the American Chemical Society, 130(28), 8884–8885. https://doi.org/10.1021/ja802691e
Götte,, M., Marquet,, R., Isel,, C., Anderson,, V. E., Keith,, G., Gross,, H. J., … Heumann,, H. (1996). Probing the higher order structure of RNA with peroxonitrous acid. FEBS Letters, 390(2), 226–228.
Greber,, B. J., Boehringer,, D., Leibundgut,, M., Bieri,, P., Leitner,, A., Schmitz,, N., … Ban,, N. (2014). The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature, 515(7526), 283–286. https://doi.org/10.1038/nature13895
Günzl,, A., Palfi,, Z., & Bindereif,, A. (2002). Analysis of RNA‐protein complexes by oligonucleotide‐targeted RNase H digestion. Methods, 26(2), 162–169. https://doi.org/10.1016/S1046‐2023(02)00019‐1
Guo,, J. U., & Bartel,, D. P. (2016). RNA G‐quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science, 353(6306), aaf5371–aaf5371. https://doi.org/10.1126/science.aaf5371
Gutell,, R. R. (1993). Comparative studies of RNA: Inferring higher‐order structure from patterns of sequence variation. Current Opinion in Structural Biology, 3(3), 313–322. https://doi.org/10.1016/S0959-440X(05)80101-0
Hang,, J., Wan,, R., Yan,, C., & Shi,, Y. (2015). Structural basis of pre‐mRNA splicing. Science, 349(6253), 1191–1198. https://doi.org/10.1126/science.aac8159
Hansen,, K. D., Brenner,, S. E., & Dudoit,, S. (2010). Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research, 38(12), e131. https://doi.org/10.1093/nar/gkq224
Helwak,, A., Kudla,, G., Dudnakova,, T., & Tollervey,, D. (2013). Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153(3), 654–665. https://doi.org/10.1016/j.cell.2013.03.043
Hoernes,, T. P., Clementi,, N., Juen,, M. A., Shi,, X., Faserl,, K., Willi,, J., … Erlacher,, M. D. (2018). Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor‐mediated peptide release. Proceedings of the National Academy of Sciences of the USA, 115(3), E382–E389. https://doi.org/10.1073/pnas.1714554115
Homan,, P. J., Favorov,, O. V., Lavender,, C. a., Kursun,, O., Ge,, X., Busan,, S., … Weeks,, K. M. (2014). Single‐molecule correlated chemical probing of RNA. Proceedings of the National Academy of Sciences of the USA, 111(38), 13858–13863. https://doi.org/10.1073/pnas.1407306111
Incarnato,, D., Morandi,, E., Anselmi,, F., Simon,, L. M., Basile,, G., & Oliviero,, S. (2017). In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding. Nucleic Acids Research, 45(16), 9716–9725. https://doi.org/10.1093/nar/gkx617
Incarnato,, D., Neri,, F., Anselmi,, F., & Oliviero,, S. (2014). Genome‐wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biology, 15(10), 491. https://doi.org/10.1186/s13059-014-0491-2
Ingolia,, N. T., Ghaemmaghami,, S., Newman,, J. R. S., & Weissman,, J. S. (2009). Genome‐wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924), 218–223. https://doi.org/10.1126/science.1168978
Isel,, C., Westhof,, E., Massire,, C., Grice,, S. F., Ehresmann,, B., Ehresmann,, C., & Marquet,, R. (1999). Structural basis for the specificity of the initiation of HIV‐1 reverse transcription. The EMBO Journal, 18(4), 1038–1048. https://doi.org/10.1093/emboj/18.4.1038
Jayaprakash,, A. D., Jabado,, O., Brown,, B. D., & Sachidanandam,, R. (2011). Identification and remediation of biases in the activity of RNA ligases in small‐RNA deep sequencing. Nucleic Acids Research, 39(21), e141. https://doi.org/10.1093/nar/gkr693
Jayaraman,, D., & Kenyon,, J. C. (2018). New windows into retroviral RNA structures. Retrovirology, 15(1), 11. https://doi.org/10.1186/s12977-018-0393-6
Jones,, C. P., Cantara,, W. A., Olson,, E. D., & Musier‐Forsyth,, K. (2014). Small‐angle X‐ray scattering‐derived structure of the HIV‐1 5′ UTR reveals 3D tRNA mimicry. Proceedings of the National Academy of Sciences of the USA, 111(9), 3395–3400. https://doi.org/10.1073/pnas.1319658111
Juan,, V., & Wilson,, C. (1999). RNA secondary structure prediction based on free energy and phylogenetic analysis. Journal of Molecular Biology, 289(4), 935–947. https://doi.org/10.1006/jmbi.1999.2801
Karabiber,, F., McGinnis,, J. L., Favorov,, O. V., & Weeks,, K. M. (2013). QuShape: Rapid, accurate, and best‐practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA, 19(1), 63–73. https://doi.org/10.1261/rna.036327.112
Keane,, S. C., Heng,, X., Lu,, K., Kharytonchyk,, S., Ramakrishnan,, V., Carter,, G., … Summers,, M. F. (2015). RNA structure. Structure of the HIV‐1 RNA packaging signal. Science, 348(6237), 917–921. https://doi.org/10.1126/science.aaa9266
Kenyon,, J. C., Prestwood,, L. J., Le Grice,, S. F. J., & Lever,, A. M. L. (2013). In‐gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV‐1 leader. Nucleic Acids Research, 41(18), e174. https://doi.org/10.1093/nar/gkt690
Kertesz,, M., Wan,, Y., Mazor,, E., Rinn,, J. L., Nutter,, R. C., Chang,, H. Y., & Segal,, E. (2010). Genome‐wide measurement of RNA secondary structure in yeast. Nature, 467(7311), 103–107. https://doi.org/10.1038/nature09322
Kharytonchyk,, S., Monti,, S., Smaldino,, P. J., Van,, V., Bolden,, N. C., Brown,, J. D., … Summers,, M. F. (2016). Transcriptional start site heterogeneity modulates the structure and function of the HIV‐1 genome. Proceedings of the National Academy of Sciences of the USA, 113(47), 13378–13383. https://doi.org/10.1073/pnas.1616627113
Kielpinski,, L. J., & Vinther,, J. (2014). Massive parallel‐sequencing‐based hydroxyl radical probing of RNA accessibility. Nucleic Acids Research, 42(8), e70. https://doi.org/10.1093/nar/gku167
Kladwang,, W., Mann,, T. H., Becka,, A., Tian,, S., Kim,, H., Yoon,, S., & Das,, R. (2014). Standardization of RNA chemical mapping experiments. Biochemistry, 53, 3063–3065. https://doi.org/10.1021/bi5003426
Kladwang,, W., VanLang,, C. C., Cordero,, P., & Das,, R. (2011). A two‐dimensional mutate‐and‐map strategy for non‐coding RNA structure. Nature Chemistry, 3(12), 954–962. https://doi.org/10.1038/nchem.1176
Kozak,, M. (2005). Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene, 361(1–2), 13–37. https://doi.org/10.1016/j.gene.2005.06.037
Kozarewa,, I., Ning,, Z., Quail,, M. A., Sanders,, M. J., Berriman,, M., & Turner,, D. J. (2009). Amplification‐free Illumina sequencing‐library preparation facilitates improved mapping and assembly of (G+C)‐biased genomes. Nature Methods, 6(4), 291–295. https://doi.org/10.1038/nmeth.1311
Krokhotin,, A., Mustoe,, A. M., Weeks,, K. M., & Dokholyan,, N. V. (2017). Direct identification of base‐paired RNA nucleotides by correlated chemical probing. RNA, 23(1), 6–13. https://doi.org/10.1261/rna.058586.116
Kudla,, G., Granneman,, S., Hahn,, D., Beggs,, J. D., & Tollervey,, D. (2011). Cross‐linking, ligation, and sequencing of hybrids reveals RNA‐RNA interactions in yeast. Proceedings of the National Academy of Sciences of the USA, 108(24), 10010–10015. https://doi.org/10.1073/pnas.1017386108
Kutchko,, K., & Laederach,, A. (2017). Transcending the prediction paradigm: Novel applications of SHAPE to RNA function and evolution. WIREs RNA, 8, e1374. https://doi.org/10.1002/wrna.1374
Kwok,, C. K. (2016). Dawn of the in vivo RNA structurome and interactome. Biochemical Society Transactions, 44(5), 1395–1410. https://doi.org/10.1042/BST20160075
Kwok,, C. K., Ding,, Y., Tang,, Y., Assmann,, S. M., & Bevilacqua,, P. C. (2013). Determination of in vivo RNA structure in low‐abundance transcripts. Nature Communications, 4, 2971. https://doi.org/10.1038/ncomms3971
Ledda,, M., & Aviran,, S. (2018). PATTERNA: Transcriptome‐wide search for functional RNA elements via structural data signatures. Genome Biology, 19(1), 28. https://doi.org/10.1186/s13059-018-1399-z
Lee,, B., Flynn,, R. A., Kadina,, A., Guo,, J. K., Kool,, E. T., & Chang,, H. Y. (2017). Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA, 23(2), 169–174. https://doi.org/10.1261/rna.058784.116
Li,, H., & Aviran,, S. (2018). Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nature Communications, 9, 606. https://doi.org/10.1038/s41467-018-02923-8
Lorenz,, R., Bernhart,, S. H., Höner Zu Siederdissen,, C., Tafer,, H., Flamm,, C., Stadler,, P. F., & Hofacker,, I. L. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6, 26. https://doi.org/10.1186/1748-7188-6-26
Loughrey,, D., Watters,, K. E., Settle,, A. H., & Lucks,, J. B. (2014). SHAPE‐Seq 2.0: Systematic optimization and extension of high‐throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic Acids Research, 42(21), 1–10. https://doi.org/10.1093/nar/gku909
Low,, J. T., & Weeks,, K. M. (2010). SHAPE‐directed RNA secondary structure prediction. Methods, 52(2), 150–158. https://doi.org/10.1016/j.ymeth.2010.06.007
Lu,, K., Heng,, X., Garyu,, L., Monti,, S., Garcia,, E. L., Kharytonchyk,, S., … Summers,, M. F. (2011). NMR detection of structures in the HIV‐1 5′‐leader RNA that regulate genome packaging. Science, 334(6053), 242–245. https://doi.org/10.1126/science.1210460
Lu,, Z., Zhang,, Q. C., Lee,, B., Flynn,, R. A., Smith,, M. A., Robinson,, J. T., … Chang,, H. Y. (2016). RNA duplex map in living cells reveals higher‐order transcriptome structure. Cell, 165(5), 1267–1279. https://doi.org/10.1016/j.cell.2016.04.028
Lucks,, J. B., Mortimer,, S. A., Trapnell,, C., Luo,, S., Aviran,, S., Schroth,, G. P., … Arkin,, A. P. (2011). Multiplexed RNA structure characterization with selective 2′‐hydroxyl acylation analyzed by primer extension sequencing (SHAPE‐Seq). Proceedings of the National Academy of Sciences of the USA, 108(27), 11063–11068. https://doi.org/10.1073/pnas.1106501108
Lusvarghi,, S., Sztuba‐Solinska,, J., Purzycka,, K. J., Pauly,, G. T., Rausch,, J. W., & Le Grice,, S. F. J. (2013). The HIV‐2 rev‐response element: Determining secondary structure and defining folding intermediates. Nucleic Acids Research, 41(13), 6637–6649. https://doi.org/10.1093/nar/gkt353
Mailler,, E., Bernacchi,, S., Marquet,, R., Paillart,, J.‐C., Vivet‐Boudou,, V., & Smyth,, R. P. (2016). The life‐cycle of the HIV‐1 gag‐RNA complex. Viruses, 8(9), 248. https://doi.org/10.3390/v8090248
Mandiyan,, V., & Boublik,, M. (1990). Structural analysis of the 5′ domain of the HeLa 18S ribosomal RNA by chemical and enzymatic probing. Nucleic Acids Research, 18(23), 7055–7062.
Martin,, K. C., & Ephrussi,, A. (2009). mRNA localization: Gene expression in the spatial dimension. Cell, 136(4), 719–730. https://doi.org/10.1016/j.cell.2009.01.044
Masquida,, B., Sauter,, C., & Westhof,, E. (1999). A sulfate pocket formed by three GoU pairs in the 0.97 a resolution X‐ray structure of a nonameric RNA. RNA, 5(10), 1384–1395.
Mauger,, D. M., Golden,, M., Yamane,, D., Williford,, S., Lemon,, S. M., Martin,, D. P., & Weeks,, K. M. (2015). Functionally conserved architecture of hepatitis C virus RNA genomes. Proceedings of the National Academy of Sciences of the USA, 112(12), 3692–3697. https://doi.org/10.1073/pnas.1416266112
Mauger,, D. M., Siegfried,, N. A., & Weeks,, K. M. (2013). The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Letters, 587(8), 1180–1188. https://doi.org/10.1016/j.febslet.2013.03.002
McGinnis,, J. L., Dunkle,, J. A., Cate,, J. H. D., & Weeks,, K. M. (2012). The mechanisms of RNA SHAPE chemistry. Journal of the American Chemical Society, 134(15), 6617–6624. https://doi.org/10.1021/ja2104075
McManus,, C. J., & Graveley,, B. R. (2011). RNA structure and the mechanisms of alternative splicing. Current Opinion in Genetics %26 Development, 21(4), 373–379. https://doi.org/10.1016/j.gde.2011.04.001
Merino,, E. J., Wilkinson,, K. A., Coughlan,, J. L., & Weeks,, K. M. (2005). RNA structure analysis at single nucleotide resolution by selective 2′‐hydroxyl acylation and primer extension (SHAPE). Journal of the American Chemical Society, 127(12), 4223–4231. https://doi.org/10.1021/ja043822v
Miao,, Z., Adamiak,, R. W., Antczak,, M., Batey,, R. T., Becka,, A. J., Biesiada,, M., … Westhof,, E. (2017). RNA‐puzzles round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, 23(5), 655–672. https://doi.org/10.1261/rna.060368.116
Miao,, Z., Adamiak,, R. W., Blanchet,, M.‐F., Boniecki,, M., Bujnicki,, J. M., Chen,, S.‐J., … Westhof,, E. (2015). RNA‐puzzles round II: Assessment of RNA structure prediction programs applied to three large RNA structures. RNA, 21(6), 1066–1084. https://doi.org/10.1261/rna.049502.114
Miao,, Z., & Westhof,, E. (2017). RNA structure: Advances and assessment of 3D structure prediction. Annual Review of Biophysics, 46, 483–503. https://doi.org/10.1146/annurev‐biophys‐070816‐034125
Michel,, F., Costa,, M., Massire,, C., & Westhof,, E. (2000). Modeling RNA tertiary structure from patterns of sequence variation. Methods in Enzymology, 317, 491–510.
Michel,, F., & Westhof,, E. (1990). Modelling of the three‐dimensional architecture of group I catalytic introns based on comparative sequence analysis. Journal of Molecular Biology, 216(3), 585–610. https://doi.org/10.1016/0022-2836(90)90386-Z
Mitra,, S., Shcherbakova,, I. V., Altman,, R. B., Brenowitz,, M., & Laederach,, A. (2008). High‐throughput single‐nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Research, 36(11), e63. https://doi.org/10.1093/nar/gkn267
Mohr,, S., Ghanem,, E., Smith,, W., Sheeter,, D., Qin,, Y., King,, O., … Lambowitz,, A. M. (2013). Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next‐generation RNA sequencing. RNA, 19(7), 958–970. https://doi.org/10.1261/rna.039743.113
Morris,, K. V., & Mattick,, J. S. (2014). The rise of regulatory RNA. Nature Reviews Genetics, 15(6), 423–437. https://doi.org/10.1038/nrg3722
Mortimer,, S. A., Kidwell,, M. A., & Doudna,, J. A. (2014). Insights into RNA structure and function from genome‐wide studies. Nature Reviews Genetics, 15, 469–479. https://doi.org/10.1038/nrg3681
Mortimer,, S. A., & Weeks,, K. M. (2007). A fast‐acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. Journal of the American Chemical Society, 129(14), 4144–4145. https://doi.org/10.1021/ja0704028
Natchiar,, S. K., Myasnikov,, A. G., Kratzat,, H., Hazemann,, I., & Klaholz,, B. P. (2017). Visualization of chemical modifications in the human 80S ribosome structure. Nature, 551(7681), 472–477. https://doi.org/10.1038/nature24482
Nguyen,, T. C., Cao,, X., Yu,, P., Xiao,, S., Lu,, J., Biase,, F. H., … Zhong,, S. (2016). Mapping RNA‐RNA interactome and RNA structure in vivo by MARIO. Nature Communications, 7, 12023. https://doi.org/10.1038/ncomms12023
Nguyen,, T. H. D., Galej,, W. P., Bai,, X., Savva,, C. G., Newman,, A. J., Scheres,, S. H. W., & Nagai,, K. (2015). The architecture of the spliceosomal U4/U6.U5 tri‐snRNP. Nature, 523(7558), 47–52. https://doi.org/10.1038/nature14548
Oyola,, S. O., Otto,, T. D., Gu,, Y., Maslen,, G., Manske,, M., Campino,, S., … Quail,, M. A. (2012). Optimizing Illumina next‐generation sequencing library preparation for extremely AT‐biased genomes. BMC Genomics, 13(1), 1. https://doi.org/10.1186/1471-2164-13-1
Paillart,, J. C., Dettenhofer,, M., Yu,, X. F., Ehresmann,, C., Ehresmann,, B., & Marquet,, R. (2004). First snapshots of the HIV‐1 RNA structure in infected cells and in virions. Journal of Biological Chemistry, 279, 48397–48403. https://doi.org/10.1074/jbc.M408294200
Pang,, P. S., Elazar,, M., Pham,, E. A., & Glenn,, J. S. (2011). Simplified RNA secondary structure mapping by automation of SHAPE data analysis. Nucleic Acids Research, 39(22), e151. https://doi.org/10.1093/nar/gkr773
Peattie,, D. A., & Gilbert,, W. (1980). Chemical probes for higher‐order structure in RNA. Proceedings of the National Academy of Sciences of the USA, 77(8), 4679–4682. https://doi.org/10.1073/pnas.77.8.4679
Piao,, M., Sun,, L., & Zhang,, Q. C. (2017). RNA regulations and functions decoded by transcriptome‐wide RNA structure probing. Genomics, Proteomics, %26 Bioinformatics, 15(5), 267–278. https://doi.org/10.1016/j.gpb.2017.05.002
Pirakitikulr,, N., Kohlway,, A., Lindenbach,, B. D., & Pyle,, A. M. (2016). The coding region of the HCV genome contains a network of regulatory RNA structures. Molecular Cell, 62(1), 111–120. https://doi.org/10.1016/j.molcel.2016.01.024
Poulsen,, L. D., Kielpinski,, L. J., Salama,, S. R., Krogh,, A., & Vinther,, J. (2015). SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing‐based probing data. RNA, 21(5), 1042–1052. https://doi.org/10.1261/rna.047068.114
Proctor,, J. R., & Meyer,, I. M. (2013). COFOLD: An RNA secondary structure prediction method that takes co‐transcriptional folding into account. Nucleic Acids Research, 41(9), e102. https://doi.org/10.1093/nar/gkt174
Qu,, H. L., Michot,, B., & Bachellerie,, J. P. (1983). Improved methods for structure probing in large RNAs: A rapid « heterologous » sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5′ terminal domain of eukaryotic 28S rRNA. Nucleic Acids Research, 11(17), 5903–5920.
Ramani,, V., Qiu,, R., & Shendure,, J. (2015). High‐throughput determination of RNA structure by proximity ligation. Nature Biotechnology, 33(9), 980–984. https://doi.org/10.1038/nbt.3289
Rausch,, J. W., Sztuba‐Solinska,, J., & Grice,, S. F. J. (2017). Probing the structures of viral RNA regulatory elements with SHAPE and related methodologies. Frontiers in Microbiology, 8, 2634. https://doi.org/10.3389/fmicb.2017.02634
Regulski,, E. E., & Breaker,, R. R. (2008). In‐line probing analysis of riboswitches. Methods in Molecular Biology, 419, 53–67. https://doi.org/10.1007/978‐1‐59745‐033‐1_4
Reuter,, J. S., & Mathews,, D. H. (2010). RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, 129. https://doi.org/10.1186/1471‐2105‐11‐129
Rice,, G. M., Leonard,, C. W., & Weeks,, K. M. (2014). RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA, 20(6), 846–854. https://doi.org/10.1261/rna.043323.113
Rouskin,, S., Zubradt,, M., Washietl,, S., Kellis,, M., & Weissman,, J. S. (2014). Genome‐wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505(7485), 701–705. https://doi.org/10.1038/nature12894
Schlegl,, J., Gegout,, V., Schläger,, B., Hentze,, M. W., Westhof,, E., Ehresmann,, C., … Romby,, P. (1997). Probing the structure of the regulatory region of human transferrin receptor messenger RNA and its interaction with iron regulatory protein‐1. RNA, 3(10), 1159–1172.
Schroeder,, S. J. (2009). Advances in RNA structure prediction from sequence: New tools for generating hypotheses about viral RNA structure‐function relationships. Journal of Virology, 83(13), 6326–6334. https://doi.org/10.1128/JVI.00251-09
Schwartz,, S., Oren,, R., & Ast,, G. (2011). Detection and removal of biases in the analysis of next‐generation sequencing reads. PLoS One, 6(1), e16685. https://doi.org/10.1371/journal.pone.0016685
Selega,, A., Sirocchi,, C., Iosub,, I., Granneman,, S., & Sanguinetti,, G. (2017). Robust statistical modeling improves sensitivity of high‐throughput RNA structure probing experiments. Nature Methods, 14(1), 83–89. https://doi.org/10.1038/nmeth.4068
Serganov,, A., & Patel,, D. J. (2007). Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins. Nature Reviews Genetics, 8(10), 776–790. https://doi.org/10.1038/nrg2172
Sexton,, A. N., Wang,, P. Y., Rutenberg‐Schoenberg,, M., & Simon,, M. D. (2017). Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA. Biochemistry, 56(35), 4713–4721. https://doi.org/10.1021/acs.biochem.7b00323
Sharma,, E., Sterne‐Weiler,, T., O`Hanlon,, D., & Blencowe,, B. J. (2016). Global mapping of human RNA‐RNA interactions. Molecular Cell, 62(4), 618–626. https://doi.org/10.1016/j.molcel.2016.04.030
Sharp,, P. A. (2009). The centrality of RNA. Cell, 136(4), 577–580. https://doi.org/10.1016/j.cell.2009.02.007
Shiroguchi,, K., Jia,, T. Z., Sims,, P. A., & Xie,, X. S. (2012). Digital RNA sequencing minimizes sequence‐dependent bias and amplification noise with optimized single‐molecule barcodes. Proceedings of the National Academy of Sciences of the USA, 109(4), 1347–1352. https://doi.org/10.1073/pnas.1118018109
Siegfried,, N. A., Busan,, S., Rice,, G. M., Nelson,, J. A. E., & Weeks,, K. M. (2014). RNA motif discovery by SHAPE and mutational profiling (SHAPE‐MaP). Nature Methods, 11(9), 959–965. https://doi.org/10.1038/nmeth.3029
Smith,, M. R., Smyth,, R. P., Marquet,, R., & Kleist,, M. (2016). MIMEAnTo: Profiling functional RNA in mutational interference mapping experiments. Bioinformatics, 32(21), 3369–3370. https://doi.org/10.1093/bioinformatics/btw479
Smola,, M. J., Calabrese,, J. M., & Weeks,, K. M. (2015). Detection of RNA‐protein interactions in living cells with SHAPE. Biochemistry, 54(46), 6867–6875. https://doi.org/10.1021/acs.biochem.5b00977
Smola,, M. J., Rice,, G. M., Busan,, S., Siegfried,, N. A., & Weeks,, K. M. (2015). Selective 2′‐hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE‐MaP) for direct, versatile and accurate RNA structure analysis. Nature Protocols, 10(11), 1643–1669. https://doi.org/10.1038/nprot.2015.103
Smyth,, R. P., Despons,, L., Huili,, G., Bernacchi,, S., Hijnen,, M., Mak,, J., … Marquet,, R. (2015). Mutational interference mapping experiment (MIME) for studying RNA structure and function. Nature Methods, 12(9), 866–872. https://doi.org/10.1038/nmeth.3490
Smyth,, R. P., Schlub,, T. E., Grimm,, A., Venturi,, V., Chopra,, A., Mallal,, S., … Mak,, J. (2010). Reducing chimera formation during PCR amplification to ensure accurate genotyping. Gene, 469(1–2), 45–51. https://doi.org/10.1016/j.gene.2010.08.009
Somarowthu,, S., Legiewicz,, M., Chillón,, I., Marcia,, M., Liu,, F., & Pyle,, A. M. (2015). HOTAIR forms an intricate and modular secondary structure. Molecular Cell, 58(2), 353–361. https://doi.org/10.1016/j.molcel.2015.03.006
Sorefan,, K., Pais,, H., Hall,, A. E., Kozomara,, A., Griffiths‐Jones,, S., Moulton,, V., & Dalmay,, T. (2012). Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence, 3(1), 4. https://doi.org/10.1186/1758-907X-3-4
Spasic,, A., Assmann,, S. M., Bevilacqua,, P. C., & Mathews,, D. H. (2018). Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Research, 46(1), 314–323. https://doi.org/10.1093/nar/gkx1057
Spitale,, R. C., Crisalli,, P., Flynn,, R. A., Torre,, E. A., Kool,, E. T., & Chang,, H. Y. (2013). RNA SHAPE analysis in living cells. Nature Chemical Biology, 9(1), 18–20. https://doi.org/10.1038/nchembio.1131
Spitale,, R. C., Flynn,, R. A., Torre,, E. A., Kool,, E. T., & Chang,, H. Y. (2014). RNA structural analysis by evolving SHAPE chemistry. WIREs RNA, 5(6), 867–881. https://doi.org/10.1002/wrna.1253
Spitale,, R. C., Flynn,, R. A., Zhang,, Q. C., Crisalli,, P., Lee,, B., Jung,, J.‐W., … Chang,, H. Y. (2015). Structural imprints in vivo decode RNA regulatory mechanisms. Nature, 519(7544), 486–490. https://doi.org/10.1038/nature14263
Sükösd,, Z., Swenson,, S., Kjems,, J., & Heitsch,, C. (2013). Evaluating the accuracy of SHAPE‐directed RNA secondary structure predictions. Nucleic Acids Research, 41(5), 2807–2816. https://doi.org/10.1093/nar/gks1283
Sun,, G., Wu,, X., Wang,, J., Li,, H., Li,, X., Gao,, H., … Yen,, Y. (2011). A bias‐reducing strategy in profiling small RNAs using Solexa. RNA, 17(12), 2256–2262. https://doi.org/10.1261/rna.028621.111
Tahi,, F., Tran,, V. D. T., & Boucheham,, A. (2017). In silico prediction of RNA secondary structure. Methods in Molecular Biology, 1543, 145–168. https://doi.org/10.1007/978‐1‐4939‐6716‐2_7
Talkish,, J., May,, G., Lin,, Y., Woolford,, J. L., & McManus,, C. J. (2014). Mod‐seq: High‐throughput sequencing for chemical probing of RNA structure. RNA, 20(5), 713–720. https://doi.org/10.1261/rna.042218.113
Tang,, Y., Bouvier,, E., Kwok,, C. K., Ding,, Y., Nekrutenko,, A., Bevilacqua,, P. C., & Assmann,, S. M. (2015). StructureFold: Genome‐wide RNA secondary structure mapping and reconstruction in vivo. Bioinformatics, 31(16), 2668–2675. https://doi.org/10.1093/bioinformatics/btv213
Tian,, S., Cordero,, P., Kladwang,, W., & Das,, R. (2014). High‐throughput mutate‐map‐rescue evaluates SHAPE‐directed RNA structure and uncovers excited states. RNA, 20(11), 1815–1826. https://doi.org/10.1261/rna.044321.114
Tian,, S., & Das,, R. (2016). RNA structure through multidimensional chemical mapping. Quarterly Reviews of Biophysics, 49(37), e7. https://doi.org/10.1017/S0033583516000020
Tijerina,, P., Mohr,, S., & Russell,, R. (2007). DMS footprinting of structured RNAs and RNA‐protein complexes. Nature Protocols, 2(10), 2608–2623. https://doi.org/10.1038/nprot.2007.380
Tullius,, T. D., & Greenbaum,, J. A. (2005). Mapping nucleic acid structure by hydroxyl radical cleavage. Current Opinion in Chemical Biology, 9(2), 127–134. https://doi.org/10.1016/j.cbpa.2005.02.009
Tyrrell,, J., McGinnis,, J. L., Weeks,, K. M., & Pielak,, G. J. (2013). The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry, 52(48), 8777–8785. https://doi.org/10.1021/bi401207q
Underwood,, J. G., Uzilov,, A., Katzman,, S., Onodera,, C. S., Mainzer,, J. E., Mathews,, D. H., … Haussler,, D. (2010). FragSeq: Transcriptome‐wide RNA structure probing using high‐throughput sequencing. Nature Methods, 7(12), 995–1001. https://doi.org/10.1038/nmeth.1529
van Gurp,, T. P., McIntyre,, L. M., & Verhoeven,, K. J. F. (2013). Consistent errors in first strand cDNA due to random hexamer mispriming. PLoS One, 8(12), e85583. https://doi.org/10.1371/journal.pone.0085583
Vasa,, S. M., Guex,, N., Wilkinson,, K. A., Weeks,, K. M., & Giddings,, M. C. (2008). ShapeFinder: A software system for high‐throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA, 14(10), 1979–1990. https://doi.org/10.1261/rna.1166808
Vlassov,, V. V., Giege,, R., & Ebel,, J. P. (1980). The tertiary structure of yeast tRNAPhe in solution studied by phosphodiester bond modification with ethylnitrosourea. FEBS Letters, 120(1), 12–16.
Wan,, Y., Qu,, K., Ouyang,, Z., & Chang,, H. Y. (2013). Genome‐wide mapping of RNA structure using nuclease digestion and high‐throughput sequencing. Nature Protocols, 8(5), 849–869. https://doi.org/10.1038/nprot.2013.045
Wan,, Y., Qu,, K., Ouyang,, Z., Kertesz,, M., Li,, J., Tibshirani,, R., … Chang,, H. Y. (2012). Genome‐wide measurement of RNA folding energies. Molecular Cell, 48(2), 169–181. https://doi.org/10.1016/j.molcel.2012.08.008
Wan,, Y., Qu,, K., Zhang,, Q. C., Flynn,, R. A., Manor,, O., Ouyang,, Z., … Chang,, H. Y. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505(7485), 706–709. https://doi.org/10.1038/nature12946
Warf,, M. B., & Berglund,, J. A. (2010). Role of RNA structure in regulating pre‐mRNA splicing. Trends in Biochemical Sciences, 35(3), 169–178. https://doi.org/10.1016/j.tibs.2009.10.004
Washietl,, S., Hofacker,, I. L., Stadler,, P. F., & Kellis,, M. (2012). RNA folding with soft constraints: Reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Research, 40(10), 4261–4272. https://doi.org/10.1093/nar/gks009
Watters,, K. E., Abbott,, T. R., & Lucks,, J. B. (2016). Simultaneous characterization of cellular RNA structure and function with in‐cell SHAPE‐Seq. Nucleic Acids Research, 44(2), e12. https://doi.org/10.1093/nar/gkv879
Watters,, K. E., Choudhary,, K., Aviran,, S., Lucks,, J. B., Perry,, K. L., & Thompson,, J. R. (2018). Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. Nucleic Acids Research, 46(5), 2573–2584. https://doi.org/10.1093/nar/gkx1273
Watters,, K. E., Yu,, A. M., Strobel,, E. J., Settle,, A. H., & Lucks,, J. B. (2016). Characterizing RNA structures in vitro and in vivo with selective 2′‐hydroxyl acylation analyzed by primer extension sequencing (SHAPE‐Seq). Methods, 103, 34–48. https://doi.org/10.1016/j.ymeth.2016.04.002
Watts,, J. M., Dang,, K. K., Gorelick,, R. J., Leonard,, C. W., Bess,, J. W., Swanstrom,, R., … Weeks,, K. M. (2009). Architecture and secondary structure of an entire HIV‐1 RNA genome. Nature, 460(7256), 711–716. https://doi.org/10.1038/nature08237
Weidmann,, C. A., Mustoe,, A. M., & Weeks,, K. M. (2016). Direct duplex detection: An emerging tool in the RNA structure analysis toolbox. Trends in Biochemical Sciences, 41(9), 734–736. https://doi.org/10.1016/j.tibs.2016.07.001
Wery,, M., Descrimes,, M., Thermes,, C., Gautheret,, D., & Morillon,, A. (2013). Zinc‐mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA‐Seq. Methods, 63(1), 25–31. https://doi.org/10.1016/j.ymeth.2013.03.009
Westhof,, E., & Romby,, P. (2010). The RNA structurome: High‐throughput probing. Nature Methods, 7(12), 965–967. https://doi.org/10.1038/nmeth1210-965
Wilkinson,, K. a., Gorelick,, R. J., Vasa,, S. M., Guex,, N., Rein,, A., Mathews,, D. H., … Weeks,, K. M. (2008). High‐throughput SHAPE analysis reveals structures in HIV‐1 genomic RNA strongly conserved across distinct biological states. PLoS Biology, 6(4), e96. https://doi.org/10.1371/journal.pbio.0060096
Yoon,, S., Kim,, J., Hum,, J., Kim,, H., Park,, S., Kladwang,, W., & Das,, R. (2011). HiTRACE: High‐throughput robust analysis for capillary electrophoresis. Bioinformatics, 27(13), 1798–1805. https://doi.org/10.1093/bioinformatics/btr277
Zhao,, P., Zhang,, W., & Chen,, S.‐J. (2011). Cotranscriptional folding kinetics of ribonucleic acid secondary structures. The Journal of Chemical Physics, 135(24), 245101. https://doi.org/10.1063/1.3671644
Zheng,, Q., Ryvkin,, P., Li,, F., Dragomir,, I., Valladares,, O., Yang,, J., … Gregory,, B. (2010). Genome‐wide double‐stranded RNA sequencing reveals the functional significance of base‐paired RNAs in Arabidopsis. PLoS Genetics, 6(9), e1001141. https://doi.org/10.1371/journal.pgen.1001141
Zheng,, W., Chung,, L. M., & Zhao,, H. (2011). Bias detection and correction in RNA‐sequencing data. BMC Bioinformatics, 12(1), 290. https://doi.org/10.1186/1471‐2105‐12‐290
Zhuang,, F., Fuchs,, R. T., Sun,, Z., Zheng,, Y., & Robb,, G. B. (2012). Structural bias in T4 RNA ligase‐mediated 3′‐adapter ligation. Nucleic Acids Research, 40(7), e54. https://doi.org/10.1093/nar/gkr1263
Zubradt,, M., Gupta,, P., Persad,, S., Lambowitz,, A. M., Weissman,, J. S., & Rouskin,, S. (2017). DMS‐MaPseq for genome‐wide or targeted RNA structure probing in vivo. Nature Methods, 14(1), 75–82. https://doi.org/10.1038/nmeth.4057
Zuker,, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31(13), 3406–3415.