The molecular structure of long non-coding RNAs: emerging patterns and functional implications

References

• Adams RL, Huston NC, Tavares RCA, Pyle AM. 2019. Chapter Twelve - sensitive detection of structural features and rearrangements in long, structured RNA molecules. In: Hargrove AE, editor. Methods Enzymol. Cambridge (UK), Massachusetts (MA): Academic Press, Elsevier; p. 249–289. DOI: 10.1016/bs.mie.2019.04.002. https://en.wikipedia.org/wiki/Methods_in_Enzymology
   Google Scholar
• Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. 2018. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol. 74(Pt 9):814–840.
   PubMedGoogle Scholar
• Ahl V, Keller H, Schmidt S, Weichenrieder O. 2015. Retrotransposition and crystal structure of an alu RNP in the ribosome-stalling conformation. Mol Cell. 60(5):715–727.
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410.
   PubMed Web of Science ®Google Scholar
• Arora R, Lee Y, Wischnewski H, Brun CM, Schwarz T, Azzalin CM. 2014. RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat Commun. 5:5220.
   PubMed Web of Science ®Google Scholar
• Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. 2007. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science. 318(5851):798–801.
   PubMed Web of Science ®Google Scholar
• Balk B, Maicher A, Dees M, Klermund J, Luke-Glaser S, Bender K, Luke B. 2013. Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat Struct Mol Biol. 20(10):1199–1205.
   PubMed Web of Science ®Google Scholar
• Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, et al. 2014. Considerations when investigating lncRNA function in vivo. Elife. 3:e03058.
   PubMed Web of Science ®Google Scholar
• Batey RT, Kieft JS. 2007. Improved native affinity purification of RNA. RNA. 13(8):1384–1389.
   PubMed Web of Science ®Google Scholar
• Bellaousov S, Mathews DH. 2010. ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA. 16(10):1870–1880.
   PubMed Web of Science ®Google Scholar
• Beniaminov A, Westhof E, Krol A. 2008. Distinctive structures between chimpanzee and human in a brain noncoding RNA. RNA. 14(7):1270–1275.
   PubMed Web of Science ®Google Scholar
• Bettin N, Oss Pegorar C, Cusanelli E. 2019. The emerging roles of TERRA in telomere maintenance and genome stability. Cells. 8(3):246.
   Web of Science ®Google Scholar
• Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA. 2011. Correlating SHAPE signatures with three-dimensional RNA structures. RNA. 17(9):1688–1696.
   PubMed Web of Science ®Google Scholar
• Blythe AJ, Fox AH, Bond CS. 2016. The ins and outs of lncRNA structure: how, why and what comes next? Biochim Biophys Acta. 1859(1):46–58.
   PubMed Web of Science ®Google Scholar
• Bonasio R, Shiekhattar R. 2014. Regulation of transcription by long noncoding RNAs. Annu Rev Genet. 48:433–455.
   PubMed Web of Science ®Google Scholar
• Brannan CI, Dees EC, Ingram RS, Tilghman SM. 1990. The product of the H19 gene may function as an RNA. Mol Cell Biol. 10(1):28–36.
   PubMed Web of Science ®Google Scholar
• Brenowitz M, Chance MR, Dhavan G, Takamoto K. 2002. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting. Curr Opin Struct Biol. 12(5):648–653.
   PubMed Web of Science ®Google Scholar
• Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HF. 1992. The human xist gene - analysis of a 17 Kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell. 71(3):527–542.
   PubMed Web of Science ®Google Scholar
• Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. 2014. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nat Struct Mol Biol. 21(7):633–640.
   PubMed Web of Science ®Google Scholar
• Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. 2012. Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENbeta noncoding RNAs. Proc Natl Acad Sci USA. 109(47):19202–19207.
   PubMed Web of Science ®Google Scholar
• Brunger AT. 1997. Chapter 19, free R value: cross-validation in crystallography. In Methods in enzymology. Cambridge (UK), Massachusetts (MA): Academic Press, Elsevier; p. 366–396. DOI: 10.1016/s0076-6879(97)77021-6. https://en.wikipedia.org/wiki/Methods_in_Enzymology
   Google Scholar
• Busan S, Weeks KM. 2017. Visualization of RNA structure models within the integrative genomics viewer. RNA. 23(7):1012–1018.
   PubMed Web of Science ®Google Scholar
• Busan S, Weidmann CA, Sengupta A, Weeks KM. 2019. Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry. 58(23):2655–2664.
   PubMed Web of Science ®Google Scholar
• Butcher SE, Pyle AM. 2011. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res. 44(12):1302–1311.
   PubMed Web of Science ®Google Scholar
• Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. 2015. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 16(1):20.
   PubMedGoogle Scholar
• Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25(18):1915–1927.
   PubMed Web of Science ®Google Scholar
• Carlevaro-Fita J, Johnson R. 2019. Global positioning system: understanding long noncoding rnas through subcellular localization. Mol Cell. 73(5):869–883.
   PubMed Web of Science ®Google Scholar
• Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science. 309(5740):1559–1563.
   PubMed Web of Science ®Google Scholar
• Chakraborty S, Deb A, Maji RK, Saha S, Ghosh Z. 2014. LncRBase: an enriched resource for lncRNA information. PloS One. 9(9):e108010.
   PubMed Web of Science ®Google Scholar
• Chaulk SG, Thede GL, Kent OA, Xu Z, Gesner EM, Veldhoen RA, Khanna SK, Goping IS, MacMillan AM, Mendell JT, et al. 2011. Role of pri-miRNA tertiary structure in miR-17 ∼ 92 miRNA biogenesis. RNA Biol. 8(6):1105–1114.
   PubMed Web of Science ®Google Scholar
• Cheng CY, Kladwang W, Yesselman JD, Das R. 2017. RNA structure inference through chemical mapping after accidental or intentional mutations. Proc Natl Acad Sci USA. 114(37):9876–9881.
   PubMed Web of Science ®Google Scholar
• Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 308(5725):1149–1154.
   PubMed Web of Science ®Google Scholar
• Chillon I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM. 2015. Native purification and analysis of long RNAs. Methods Enzymol. 558:3–37.
   PubMed Web of Science ®Google Scholar
• Chillon I, Molina-Sanchez MD, Fedorova O, Garcia-Rodriguez FM, Martinez-Abarca F, Toro N. 2014. In vitro characterization of the splicing efficiency and fidelity of the RmInt1 group II intron as a means of controlling the dispersion of its host mobile element. RNA. 20(12):2000–2010.
   PubMed Web of Science ®Google Scholar
• Chillon I, Pyle AM. 2016. Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Res. 44(19):9462–9471.
   PubMed Web of Science ®Google Scholar
• Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. 2011. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 44(4):667–678.
   PubMed Web of Science ®Google Scholar
• Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS. 2012. Genome-wide analysis of long noncoding RNA stability. Genome Res. 22(5):885–898.
   PubMed Web of Science ®Google Scholar
• Collie GW, Haider SM, Neidle S, Parkinson GN. 2010. A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res. 38(16):5569–5580.
   PubMed Web of Science ®Google Scholar
• Cordero P, Kladwang W, VanLang CC, Das R. 2012. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry. 51(36):7037–7039.
   PubMed Web of Science ®Google Scholar
• Costa M, Christian EL, Michel F. 1998. Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain V. RNA. 4(9):1055–1068.
   PubMed Web of Science ®Google Scholar
• Csorba T, Questa JI, Sun Q, Dean C. 2014. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci USA. 111(45):16160–16165.
   PubMed Web of Science ®Google Scholar
• Darty K, Denise A, Ponty Y. 2009. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics. 25(15):1974–1975.
   PubMed Web of Science ®Google Scholar
• Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. 2005. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA. 11(3):344–354.
   PubMed Web of Science ®Google Scholar
• Dasgupta B, Miyashita O, Tama F. 2020. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj. 1864(2):129420.
   PubMed Web of Science ®Google Scholar
• Davidovich C, Wang X, Cifuentes-Rojas C, Goodrich KJ, Gooding AR, Lee JT, Cech TR. 2015. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Molecular Cell. 57(3):552–558.
   PubMed Web of Science ®Google Scholar
• Davidovich C, Zheng L, Goodrich KJ, Cech TR. 2013. Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol. 20(11):1250–1257.
   PubMed Web of Science ®Google Scholar
• Deigan KE, Li TW, Mathews DH, Weeks KM. 2009. Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci USA. 106(1):97–102.
   PubMed Web of Science ®Google Scholar
• Deininger P. 2011. Alu elements: know the SINEs. Genome Biol. 12(12):236.
   PubMed Web of Science ®Google Scholar
• Devereux J, Haeberli P, Smithies O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12(1 Pt 1):387–395.
   PubMed Web of Science ®Google Scholar
• Diaz-Toledano R, Ariza-Mateos A, Birk A, Martinez-Garcia B, Gomez J. 2009. In vitro characterization of a miR-122-sensitive double-helical switch element in the 5' region of hepatitis C virus RNA. Nucleic Acids Res. 37(16):5498–5510.
   PubMed Web of Science ®Google Scholar
• Diederichs S. 2014. The four dimensions of noncoding RNA conservation. Trends Genet. 30(4):121–123.
   PubMed Web of Science ®Google Scholar
• Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, et al. 2014. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol Cell. 54(5):777–790.
   PubMed Web of Science ®Google Scholar
• Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. 2014. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 505(7485):696–700.
   PubMed Web of Science ®Google Scholar
• Duszczyk MM, Wutz A, Rybin V, Sattler M. 2011. The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. RNA. 17(11):1973–1982.
   PubMed Web of Science ®Google Scholar
• Easton LE, Shibata Y, Lukavsky PJ. 2010. Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA. 16(3):647–653.
   PubMed Web of Science ®Google Scholar
• El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, et al. 2019. The Pfam protein families database in 2019. Nucleic Acids Res. 47(D1):D427–D432.
   PubMed Web of Science ®Google Scholar
• Engreitz JM, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES. 2014. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell. 159(1):188–199.
   PubMed Web of Science ®Google Scholar
• Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. 2017. Small molecule-based pattern recognition to classify RNA structure. J Am Chem Soc. 139(1):409–416.
   PubMed Web of Science ®Google Scholar
• Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. 2015. Probing xist RNA structure in cells using targeted structure-seq. PLoS Genet. 11(12):e1005668.
   PubMed Web of Science ®Google Scholar
• Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, et al. 2018. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res. 46(D1):D308–D314.
   PubMed Web of Science ®Google Scholar
• Feng X, Fu Z, Kaledhonkar S, Jia Y, Shah B, Jin A, Liu Z, Sun M, Chen B, Grassucci RA, et al. 2017. A fast and effective microfluidic spraying-plunging method for high-resolution single-particle cryo-EM. Structure. 25(4):663–670. e663.
   PubMed Web of Science ®Google Scholar
• Fernandez N, Garcia-Sacristan A, Ramajo J, Briones C, Martinez-Salas E. 2011. Structural analysis provides insights into the modular organization of picornavirus IRES. Virology. 409(2):251–261.
   PubMed Web of Science ®Google Scholar
• Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, et al. 2019. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47(D1):D766–D773.
   PubMed Web of Science ®Google Scholar
• Frieda KL, Block SM. 2012. Direct observation of cotranscriptional folding in an adenine riboswitch. Science. 338(6105):397–400.
   PubMed Web of Science ®Google Scholar
• Frohman MA, Dush MK, Martin GR. 1988. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA. 85(23):8998–9002.
   PubMed Web of Science ®Google Scholar
• Furtig B, Richter C, Wohnert J, Schwalbe H. 2003. NMR spectroscopy of RNA. Chembiochem. 4(10):936–962.
   PubMed Web of Science ®Google Scholar
• Garcia-Sacristan A, Moreno M, Ariza-Mateos A, Lopez-Camacho E, Jaudenes RM, Vazquez L, Gomez J, Martin-Gago JA, Briones C. 2015. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy. Nucleic Acids Res. 43(1):565–580.
   PubMed Web of Science ®Google Scholar
• Gomez A, Toor N. 2018. Selecting new RNA crystal contacts. Structure. 26(9):1166–1167.
   PubMed Web of Science ®Google Scholar
• Gruber AR, Bernhart SH, Lorenz R. 2015. The ViennaRNA web services. Methods Mol Biol. 1269:307–326.
   PubMedGoogle Scholar
• Haack DB, Yan XD, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N. 2019. Cryo-EM structures of a group II intron reverse splicing into DNA. Cell. 178(3):612–623.e12. +.
   PubMed Web of Science ®Google Scholar
• Hajdin CE, Ding F, Dokholyan NV, Weeks KM. 2010. On the significance of an RNA tertiary structure prediction. RNA. 16(7):1340–1349.
   PubMed Web of Science ®Google Scholar
• Hawkes EJ, Hennelly SP, Novikova IV, Irwin JA, Dean C, Sanbonmatsu KY. 2016. COOLAIR antisense RNAs form evolutionarily conserved elaborate secondary structures. Cell Rep. 16(12):3087–3096.
   PubMed Web of Science ®Google Scholar
• Hirashima K, Seimiya H. 2015. Telomeric repeat-containing RNA/G-quadruplex-forming sequences cause genome-wide alteration of gene expression in human cancer cells in vivo. Nucleic Acids Res. 43(4):2022–2032.
   PubMed Web of Science ®Google Scholar
• Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS, Batey RT. 2020. The Sox2 transcription factor binds RNA. Nat Commun. 11(1):1805.
   PubMed Web of Science ®Google Scholar
• Honer zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL. 2011. A folding algorithm for extended RNA secondary structures. Bioinformatics. 27(13):i129–136.
   PubMed Web of Science ®Google Scholar
• Hu S, Wang X, Shan G. 2016. Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing. Nat Struct Mol Biol. 23(11):1011–1019.
   PubMed Web of Science ®Google Scholar
• Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 142(3):409–419.
   PubMed Web of Science ®Google Scholar
• Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ. 2016. The Dfam database of repetitive DNA families. Nucleic Acids Res. 44(D1):D81–89.
   PubMed Web of Science ®Google Scholar
• Hudson WH, Pickard MR, de Vera IM, Kuiper EG, Mourtada-Maarabouni M, Conn GL, Kojetin DJ, Williams GT, Ortlund EA. 2014. Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate. Nat Commun. 5:5395.
   PubMed Web of Science ®Google Scholar
• Humphris-Narayanan E, Pyle AM. 2012. Discrete RNA libraries from pseudo-torsional space. J Mol Biol. 421(1):6–26.
   PubMed Web of Science ®Google Scholar
• Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. 2007. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics. 8:39.
   PubMed Web of Science ®Google Scholar
• Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, et al. 2013. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell. 51(2):156–173.
   PubMed Web of Science ®Google Scholar
• Jabbari H, Wark I, Montemagno C, Will S. 2018. Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinformatics. 34(22):3849–3856.
   PubMed Web of Science ®Google Scholar
• Jeffery CJ. 1999. Moonlighting proteins. Trends Biochem Sci. 24(1):8–11.
   PubMed Web of Science ®Google Scholar
• Jensen MR, Ruigrok RW, Blackledge M. 2013. Describing intrinsically disordered proteins at atomic resolution by NMR. Curr Opin Struct Biol. 23(3):426–435.
   PubMed Web of Science ®Google Scholar
• Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. 2018. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46(D1):D335–D342.
   PubMed Web of Science ®Google Scholar
• Kaneko S, Bonasio R, Saldana-Meyer R, Yoshida T, Son J, Nishino K, Umezawa A, Reinberg D. 2014. Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol Cell. 53(2):290–300.
   PubMed Web of Science ®Google Scholar
• Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, et al. 2020. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat Methods. 17(7):699–707.
   PubMed Web of Science ®Google Scholar
• Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 9(4):e1003470.
   PubMed Web of Science ®Google Scholar
• Karabiber F, McGinnis JL, Favorov OV, Weeks KM. 2013. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA. 19(1):63–73.
   PubMed Web of Science ®Google Scholar
• Kashi K, Henderson L, Bonetti A, Carninci P. 2016. Discovery and functional analysis of lncRNAs: methodologies to investigate an uncharacterized transcriptome. Biochim Biophys Acta. 1859(1):3–15.
   PubMed Web of Science ®Google Scholar
• Keane SC, Heng X, Lu K, Kharytonchyk S, Ramakrishnan V, Carter G, Barton S, Hosic A, Florwick A, Santos J, et al. 2015. RNA structure. Structure of the HIV-1 RNA packaging signal. Science. 348(6237):917–921.
   PubMed Web of Science ®Google Scholar
• Kent WJ. 2002. BLAT--the BLAST-like alignment tool. Genome Res. 12(4):656–664.
   PubMed Web of Science ®Google Scholar
• Kerpedjiev P, Honer Zu Siederdissen C, Hofacker IL. 2015. Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA. 21(6):1110–1121.
   PubMed Web of Science ®Google Scholar
• Khersonsky O, Roodveldt C, Tawfik DS. 2006. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr Opin Chem Biol. 10(5):498–508.
   PubMed Web of Science ®Google Scholar
• Kikin O, D'Antonio L, Bagga PS. 2006. QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34:W676–682.
   PubMed Web of Science ®Google Scholar
• Kim DN, Thiel BC, Mrozowich T, Hennelly SP, Hofacker IL, Patel TR, Sanbonmatsu KY. 2020. Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nat Commun. 11(1):148.
   PubMed Web of Science ®Google Scholar
• Kim EZ, Wespiser AR, Caffrey DR. 2016. The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. RNA. 22(2):254–264.
   PubMed Web of Science ®Google Scholar
• Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. 2010. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal. 3(107):ra8.
   PubMed Web of Science ®Google Scholar
• Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, et al. 2018. Functional classification of long non-coding RNAs by k-mer content. Nat Genet. 50(10):1474–1482.
   PubMed Web of Science ®Google Scholar
• Kladwang W, Cordero P, Das R. 2011. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA. 17(3):522–534.
   PubMed Web of Science ®Google Scholar
• Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, et al. 2013. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 152(3):570–583.
   PubMed Web of Science ®Google Scholar
• Knapp G. 1989. Enzymatic approaches to probing of RNA secondary and tertiary structure. Meth Enzymol. 180:192–212.
   PubMed Web of Science ®Google Scholar
• Kramerov DA, Vassetzky NS. 2011. Origin and evolution of SINEs in eukaryotic genomes. Heredity. 107(6):487–495.
   PubMed Web of Science ®Google Scholar
• Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J. 2007. Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet. 23(4):158–161.
   PubMed Web of Science ®Google Scholar
• Kuhlbrandt W. 2014. Cryo-EM enters a new era. eLife. 3:e03678.
   PubMed Web of Science ®Google Scholar
• Kumagai I, Takeda S, Miura K. 1992. Functional conversion of the homologous proteins alpha-lactalbumin and lysozyme by exon exchange. Proc Natl Acad Sci USA. 89(13):5887–5891.
   PubMed Web of Science ®Google Scholar
• Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29(22):4633–4642.
   PubMed Web of Science ®Google Scholar
• Laing C, Schlick T. 2009. Analysis of four-way junctions in RNA structures. J Mol Biol. 390(3):547–559.
   PubMed Web of Science ®Google Scholar
• Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, Tsai M-J, O’Malley BW. 1999. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell. 97(1):17–27.
   PubMed Web of Science ®Google Scholar
• Lavender CA, Gorelick RJ, Weeks KM. 2015. Structure-based alignment and consensus secondary structures for three HIV-related RNA genomes. PLoS Comput Biol. 11(5):e1004230.
   PubMed Web of Science ®Google Scholar
• Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. 2017. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA. 23(2):169–174.
   PubMed Web of Science ®Google Scholar
• Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30(16):3497–3531.
   PubMed Web of Science ®Google Scholar
• Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA. 7(4):499–512.
   PubMed Web of Science ®Google Scholar
• Lescoute A, Westhof E. 2006. Topology of three-way junctions in folded RNAs. RNA. 12(1):83–93.
   PubMed Web of Science ®Google Scholar
• Lewis CJ, Pan T, Kalsotra A. 2017. RNA modifications and structures cooperate to guide RNA-protein interactions. Nat Rev Mol Cell Biol. 18(3):202–210.
   PubMed Web of Science ®Google Scholar
• Li L, Liu B, Wapinski OL, Tsai M-C, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, et al. 2013. Targeted disruption of hotair leads to homeotic transformation and gene derepression. Cell Rep. 5(1):3–12.
   PubMed Web of Science ®Google Scholar
• Lin Y, Schmidt BF, Bruchez MP, McManus CJ. 2018. Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture. Nucleic Acids Res. 46(7):3742–3752.
   PubMed Web of Science ®Google Scholar
• Liu F, Somarowthu S, Pyle AM. 2017. Visualizing the secondary and tertiary architectural domains of lncRNA RepA. Nat Chem Biol. 13(3):282–289.
   PubMed Web of Science ®Google Scholar
• Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. 2015. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 518(7540):560–564.
   PubMed Web of Science ®Google Scholar
• Liu N, Zhou KI, Parisien M, Dai Q, Diatchenko L, Pan T. 2017. N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 45(10):6051–6063.
   PubMed Web of Science ®Google Scholar
• Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T. 2017. Transcriptomics technologies. PLoS Comput Biol. 13(5):e1005457.
   PubMed Web of Science ®Google Scholar
• Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, et al. 2016. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell. 165(5):1267–1279.
   PubMed Web of Science ®Google Scholar
• Lubelsky Y, Ulitsky I. 2018. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature. 555(7694):107–111.
   PubMed Web of Science ®Google Scholar
• Lyubchenko YL, Shlyakhtenko LS, Ando T. 2011. Imaging of nucleic acids with atomic force microscopy. Methods. 54(2):274–283.
   PubMed Web of Science ®Google Scholar
• Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, Dubois A, Sanglier-Cianferani S, Van Dorsselaer A, Clerc P, Avner P, et al. 2010. 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol. 8(1):e1000276.
   PubMed Web of Science ®Google Scholar
• Magnus M, Kappel K, Das R, Bujnicki JM. 2019. RNA 3D structure prediction guided by independent folding of homologous sequences. BMC Bioinformatics. 20(1):512.
   PubMed Web of Science ®Google Scholar
• Manigrasso J, Chillon I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. 2020. Visualizing group II intron dynamics between the first and second steps of splicing. Nat Commun. 11(1):2837.
   PubMed Web of Science ®Google Scholar
• Marcia M. 2016. Using molecular replacement phasing to study the structure and function of RNA. Methods Mol Biol. 1320:233–257.
   PubMedGoogle Scholar
• Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM. 2013. Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallogr D Biol Crystallogr. 69(Pt 11):2174–2185.
   PubMedGoogle Scholar
• Marcia M, Pyle AM. 2012. Visualizing group II intron catalysis through the stages of splicing. Cell. 151(3):497–507.
   PubMed Web of Science ®Google Scholar
• Markham NR, Zuker M. 2008. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 453:3–31.
   PubMedGoogle Scholar
• Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM. 1998. Protein folds and functions. Structure. 6(7):875–884.
   PubMed Web of Science ®Google Scholar
• Marusic M, Schlagnitweit J, Petzold K. 2019. RNA dynamics by NMR spectroscopy. Chembiochem. 20(21):2685–2710.
   PubMed Web of Science ®Google Scholar
• Mattick JS, Rinn JL. 2015. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol. 22(1):5–7.
   PubMed Web of Science ®Google Scholar
• Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Mele M, Rinn JL. 2019. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 29(3):344–355.
   PubMed Web of Science ®Google Scholar
• Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP, Weeks KM. 2015. Functionally conserved architecture of hepatitis C virus RNA genomes. Proc Natl Acad Sci USA. 112(12):3692–3697.
   PubMed Web of Science ®Google Scholar
• McCown PJ, Wang MC, Jaeger L, Brown JA. 2019. Secondary structural model of human MALAT1 reveals multiple structure–function relationships. IJMS. 20(22):5610.
   Google Scholar
• Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM. 2005. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc. 127(12):4223–4231.
   PubMed Web of Science ®Google Scholar
• Minks J, Baldry SE, Yang C, Cotton AM, Brown CJ. 2013. XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells. Epigenet Chromatin. 6(1):23.
   PubMedGoogle Scholar
• Minor DL, Jr., Kim PS. 1996. Context-dependent secondary structure formation of a designed protein sequence. Nature. 380(6576):730–734.
   PubMed Web of Science ®Google Scholar
• Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. 2008. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 36(11):e63.
   PubMed Web of Science ®Google Scholar
• Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. 2010. Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science. 330(6008):1244–1247.
   PubMed Web of Science ®Google Scholar
• Miyagi A, Scheuring S. 2018. A novel phase-shift-based amplitude detector for a high-speed atomic force microscope. Rev Sci Instrum. 89(8):083704.
   PubMed Web of Science ®Google Scholar
• Miyoshi N, Wagatsuma H, Wakana S, Shiroishi T, Nomura M, Aisaka K, Kohda T, Surani MA, Kaneko-Ishino T, Ishino F. 2000. Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q. Genes Cells. 5(3):211–220.
   PubMed Web of Science ®Google Scholar
• Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, Mitra S, Mohammed A, James AR, Hoberg E, et al. 2015. MEG3 long noncoding RNA regulates the TGF-beta pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 6:7743.
   PubMed Web of Science ®Google Scholar
• Mortimer SA, Weeks KM. 2007. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc. 129(14):4144–4145.
   PubMed Web of Science ®Google Scholar
• Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 29(22):2933–2935.
   PubMed Web of Science ®Google Scholar
• Naydenova K, Peet MJ, Russo CJ. 2019. Multifunctional graphene supports for electron cryomicroscopy. Proc Natl Acad Sci USA. 116(24):11718–11724.
   PubMed Web of Science ®Google Scholar
• Ng SY, Johnson R, Stanton LW. 2012. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. Embo J. 31(3):522–533.
   PubMed Web of Science ®Google Scholar
• Niina T, Fuchigami S, Takada S. 2020. Flexible Fitting of biomolecular structures to atomic force microscopy images via biased molecular simulations. J Chem Theory Comput. 16(2):1349–1358.
   PubMed Web of Science ®Google Scholar
• Noviello TMR, Di Liddo A, Ventola GM, Spagnuolo A, D’Aniello S, Ceccarelli M, Cerulo L. 2018. Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics. BMC Bioinf. 19(1):407.
   PubMedGoogle Scholar
• Novikova IV, Dharap A, Hennelly SP, Sanbonmatsu KY. 2013. 3S: shotgun secondary structure determination of long non-coding RNAs. Methods. 63(2):170–177.
   PubMed Web of Science ®Google Scholar
• Novikova IV, Hennelly SP, Sanbonmatsu KY. 2012a. Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure?. Bioarchitecture. 2(6):189–199.
   PubMedGoogle Scholar
• Novikova IV, Hennelly SP, Sanbonmatsu KY. 2012b. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 40(11):5034–5051.
   PubMed Web of Science ®Google Scholar
• Ottinger LM, Tullius TD. 2000. High-resolution in vivo footprinting of a protein − DNA complex using γ-radiation. J Am Chem Soc. 122(24):5901–5902.
   Web of Science ®Google Scholar
• Palangat M, Meier TI, Keene RG, Landick R. 1998. Transcriptional pausing at +62 of the HIV-1 nascent RNA modulates formation of the TAR RNA structure. Mol Cell. 1(7):1033–1042.
   PubMed Web of Science ®Google Scholar
• Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Betegon M, Bulkley D, Agard DA, Cheng Y. 2018. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J Struct Biol. 204(1):80–84.
   PubMed Web of Science ®Google Scholar
• Parisien M, Major F. 2008. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature. 452(7183):51–55.
   PubMed Web of Science ®Google Scholar
• Patel TR, Chojnowski G, Astha Koul A, McKenna SA, Bujnicki JM. 2017. Structural studies of RNA-protein complexes: a hybrid approach involving hydrodynamics, scattering, and computational methods. Methods. 118-119:146–162.
   PubMed Web of Science ®Google Scholar
• Perard J, Leyrat C, Baudin F, Drouet E, Jamin M. 2013. Structure of the full-length HCV IRES in solution. Nat Commun. 4(1):1612.
   PubMedGoogle Scholar
• Pereira MJ, Behera V, Walter NG. 2010. Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity. PloS One. 5(9):e12953.
   PubMed Web of Science ®Google Scholar
• Petrone J, DeFrancesco L. 2018. Small molecules get the message. Nat Biotechnol. 36(9):787–790.
   PubMed Web of Science ®Google Scholar
• Pirakitikulr N, Kohlway A, Lindenbach BD, Pyle AM. 2016. The coding region of the HCV genome contains a network of regulatory RNA structures. Mol Cell. 62(1):111–120.
   PubMed Web of Science ®Google Scholar
• Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW. 2012. Automated 3D structure composition for large RNAs. Nucleic Acids Res. 40(14):e112.
   PubMed Web of Science ®Google Scholar
• Pyle AM. 2010. The tertiary structure of group II introns: implications for biological function and evolution. Crit Rev Biochem Mol Biol. 45(3):215–232.
   PubMed Web of Science ®Google Scholar
• Pyle AM. 2014. Looking at LncRNAs with the ribozyme toolkit. Mol Cell. 56(1):13–17.
   PubMed Web of Science ®Google Scholar
• Pyle AM. 2016. Group II intron self-splicing. Annu Rev Biophys. 45:183–205.
   PubMed Web of Science ®Google Scholar
• Quinodoz S, Guttman M. 2014. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol. 24(11):651–663.
   PubMed Web of Science ®Google Scholar
• Reeder J, Giegerich R. 2004. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 5:104.
   PubMed Web of Science ®Google Scholar
• Reuter JS, Mathews DH. 2010. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 11(1):129.
   PubMedGoogle Scholar
• Rice GM, Leonard CW, Weeks KM. 2014. RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA. 20(6):846–854.
   PubMed Web of Science ®Google Scholar
• Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet. 16(6):276–277.
   PubMed Web of Science ®Google Scholar
• Rinn JL, Chang HY. 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 81:145–166.
   PubMed Web of Science ®Google Scholar
• Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 129(7):1311–1323.
   PubMed Web of Science ®Google Scholar
• Rivas E, Clements J, Eddy SR. 2017. A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. Nat Methods. 14(1):45–48.
   PubMed Web of Science ®Google Scholar
• Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH. 2004. Secondary structure models of the 3' untranslated regions of diverse R2 RNAs. RNA. 10(6):978–987.
   PubMed Web of Science ®Google Scholar
• Said N, Rieder R, Hurwitz R, Deckert J, Urlaub H, Vogel J. 2009. In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res. 37(20):e133.
   PubMed Web of Science ®Google Scholar
• Sarropoulos I, Marin R, Cardoso-Moreira M, Kaessmann H. 2019. Developmental dynamics of lncRNAs across mammalian organs and species. Nature. 571(7766):510–514.
   PubMed Web of Science ®Google Scholar
• Sato K, Kato Y, Hamada M, Akutsu T, Asai K. 2011. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics. 27(13):i85–93.
   PubMed Web of Science ®Google Scholar
• Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, et al. 2013. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2:e01749.
   PubMed Web of Science ®Google Scholar
• Schmidli C, Albiez S, Rima L, Righetto R, Mohammed I, Oliva P, Kovacik L, Stahlberg H, Braun T. 2019. Microfluidic protein isolation and sample preparation for high-resolution cryo-EM. Proc Natl Acad Sci USA. 116(30):15007–15012.
   PubMed Web of Science ®Google Scholar
• Sharon D, Tilgner H, Grubert F, Snyder M. 2013. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. 31(11):1009–1014.
   PubMed Web of Science ®Google Scholar
• Sharp JS, Becker JM, Hettich RL. 2004. Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Anal Chem. 76(3):672–683.
   PubMed Web of Science ®Google Scholar
• Shcherbakova I, Mitra S. 2009. Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. Meth Enzymol. 468:31–46.
   PubMed Web of Science ®Google Scholar
• Shcherbakova I, Mitra S, Beer RH, Brenowitz M. 2006. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 34(6):e48.
   PubMed Web of Science ®Google Scholar
• Sherpa C, Rausch JW, Le Grice SF. 2018. Structural characterization of maternally expressed gene 3 RNA reveals conserved motifs and potential sites of interaction with polycomb repressive complex 2. Nucleic Acids Res. 46(19):10432–10447.
   PubMed Web of Science ®Google Scholar
• Siegfried NA, Busan S, Rice GM, Nelson JA, Weeks KM. 2014. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods. 11(9):959–965.
   PubMed Web of Science ®Google Scholar
• Simon LM, Morandi E, Luganini A, Gribaudo G, Martinez-Sobrido L, Turner DH, Oliviero S, Incarnato D. 2019. In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs. Nucleic Acids Res. 47(13):7003–7017.
   PubMed Web of Science ®Google Scholar
• Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. 2011. The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci USA. 108(51):20497–20502.
   PubMed Web of Science ®Google Scholar
• Singh J, Hanson J, Paliwal K, Zhou Y. 2019. RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nat Commun. 10(1):5407.
   PubMedGoogle Scholar
• Sloma MF, Mathews DH. 2017. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput Biol. 13(11):e1005827.
   PubMed Web of Science ®Google Scholar
• Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. 2019. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PloS One. 14(5):e0216709.
   PubMed Web of Science ®Google Scholar
• Smola MJ, Calabrese JM, Weeks KM. 2015. Detection of RNA-protein interactions in living cells with SHAPE. Biochemistry. 54(46):6867–6875.
   PubMed Web of Science ®Google Scholar
• Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM, Calabrese JM, Weeks KM. 2016. SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc Natl Acad Sci USA. 113(37):10322–10327.
   PubMed Web of Science ®Google Scholar
• Somarowthu S, Legiewicz M, Chillon I, Marcia M, Liu F, Pyle AM. 2015. HOTAIR forms an intricate and modular secondary structure. Mol Cell. 58(2):353–361.
   PubMed Web of Science ®Google Scholar
• Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung J-W, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, et al. 2015. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 519(7544):486–490.
   PubMed Web of Science ®Google Scholar
• Spokoini-Stern R, Stamov D, Jessel H, Aharoni L, Haschke H, Giron J, Unger R, Segal E, Abu-Horowitz A, Bachelet I. 2020. Visualizing the structure and motion of the long noncoding RNA HOTAIR. RNA. 26(5):629–636.
   PubMed Web of Science ®Google Scholar
• Steen KA, Rice GM, Weeks KM. 2012. Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc. 134(32):13160–13163.
   PubMed Web of Science ®Google Scholar
• Su L, Chen L, Egli M, Berger JM, Rich A. 1999. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol. 6(3):285–292.
   PubMedGoogle Scholar
• Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. 2008. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 19(3):347–359.
   PubMed Web of Science ®Google Scholar
• Swisher J, Duarte CM, Su LJ, Pyle AM. 2001. Visualizing the solvent-inaccessible core of a group II intron ribozyme. Embo J. 20(8):2051–2061.
   PubMed Web of Science ®Google Scholar
• Swisher JF, Su LJ, Brenowitz M, Anderson VE, Pyle AM. 2002. Productive folding to the native state by a group II intron ribozyme. J Mol Biol. 315(3):297–310.
   PubMed Web of Science ®Google Scholar
• Takahashi MK, Watters KE, Gasper PM, Abbott TR, Carlson PD, Chen AA, Lucks JB. 2016. Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators. RNA. 22(6):920–933.
   PubMed Web of Science ®Google Scholar
• Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N. 2012. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 22(5):947–956.
   PubMed Web of Science ®Google Scholar
• Tavares RCA, Pyle AM, Somarowthu S. 2019. Phylogenetic analysis with improved parameters reveals conservation in lncRNA structures. J Mol Biol. 431(8):1592–1603.
   PubMed Web of Science ®Google Scholar
• Tomezsko PJ, Corbin VDA, Gupta P, Swaminathan H, Glasgow M, Persad S, Edwards MD, McIntosh L, Papenfuss AT, Emery A, et al. 2020. Determination of RNA structural diversity and its role in HIV-1 RNA splicing. Nature. 582(7812):438–442.
   PubMed Web of Science ®Google Scholar
• Toor N, Keating KS, Taylor SD, Pyle AM. 2008. Crystal structure of a self-spliced group II intron. Science. 320(5872):77–82.
   PubMed Web of Science ®Google Scholar
• Trewhella J. 2016. Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol. 40:1–7.
   PubMed Web of Science ®Google Scholar
• Trinh MH, Odorico M, Pique ME, Teulon JM, Roberts VAT, Eyck LF, Getzoff ED, Parot P, Chen SW, Pellequer JL. 2012. Computational reconstruction of multidomain proteins using atomic force microscopy data. Structure. 20(1):113–120.
   PubMed Web of Science ®Google Scholar
• Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, et al. 2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 39(6):925–938.
   PubMed Web of Science ®Google Scholar
• Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. 2010. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 329(5992):689–693.
   PubMed Web of Science ®Google Scholar
• Ulitsky I, Bartel DP. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell. 154(1):26–46.
   PubMed Web of Science ®Google Scholar
• Uroda T, Anastasakou E, Rossi A, Teulon JM, Pellequer JL, Annibale P, Pessey O, Inga A, Chillon I, Marcia M. 2019. Conserved pseudoknots in lncRNA MEG3 are essential for stimulation of the p53 pathway. Mol Cell. 75(5):982–995.
   PubMed Web of Science ®Google Scholar
• Uroda T, Chillon I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M. 2020. Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques. Nat Protoc. 15(6):2107–2139.
   PubMed Web of Science ®Google Scholar
• van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, et al. 2014. Classification of intrinsically disordered regions and proteins. Chem Rev. 114(13):6589–6631.
   PubMed Web of Science ®Google Scholar
• Vasa SM, Guex N, Wilkinson KA, Weeks KM, Giddings MC. 2008. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA. 14(10):1979–1990.
   PubMed Web of Science ®Google Scholar
• Vaziri S, Koehl P, Aviran S. 2018. Extracting information from RNA SHAPE data: Kalman filtering approach. PloS One. 13(11):e0207029.
   PubMed Web of Science ®Google Scholar
• Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. 2019. LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Res. 47(D1):D135–D139.
   PubMed Web of Science ®Google Scholar
• Waldsich C, Pyle AM. 2008. A kinetic intermediate that regulates proper folding of a group II intron RNA. J Mol Biol. 375(2):572–580.
   PubMed Web of Science ®Google Scholar
• Walters RD, Kugel JF, Goodrich JA. 2009. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life. 61(8):831–837.
   PubMed Web of Science ®Google Scholar
• Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY. 2012. Genome-wide measurement of RNA folding energies. Mol Cell. 48(2):169–181.
   PubMed Web of Science ®Google Scholar
• Wang X, Goodrich KJ, Gooding AR, Naeem H, Archer S, Paucek RD, Youmans DT, Cech TR, Davidovich C. 2017. Targeting of polycomb repressive complex 2 to RNA by short repeats of consecutive guanines. Mol Cell. 65(6):1056–1067.
   PubMed Web of Science ®Google Scholar
• Wapinski O, Chang HY. 2011. Long noncoding RNAs and human disease. Trends Cell Biol. 21(6):354–361.
   PubMed Web of Science ®Google Scholar
• Watkins AM, Rangan R, Das R. 2020. FARFAR2: improved de novo rosetta prediction of complex global RNA folds. Structure. 28(8):963–976.
   PubMed Web of Science ®Google Scholar
• Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB. 2016. Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat Struct Mol Biol. 23(12):1124–1131.
   PubMed Web of Science ®Google Scholar
• Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW, Jr., Swanstrom R, Burch CL, Weeks KM. 2009. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature. 460(7256):711–716.
   PubMed Web of Science ®Google Scholar
• Weakley SM, Wang H, Yao Q, Chen C. 2011. Expression and function of a large non-coding RNA gene XIST in human cancer. World J Surg. 35(8):1751–1756.
   PubMed Web of Science ®Google Scholar
• Weeks KM, Mauger DM. 2011. Exploring RNA structural codes with SHAPE chemistry. Acc Chem Res. 44(12):1280–1291.
   PubMed Web of Science ®Google Scholar
• Weinberg Z, Breaker RR. 2011. R2R--software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics. 12:3.
   PubMed Web of Science ®Google Scholar
• Weinberg Z, Perreault J, Meyer MM, Breaker RR. 2009. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature. 462(7273):656–659.
   PubMed Web of Science ®Google Scholar
• Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. 2010. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol. 11(3):R31.
   PubMed Web of Science ®Google Scholar
• Weldon C, Behm-Ansmant I, Hurley LH, Burley GA, Branlant C, Eperon IC, Dominguez C. 2017. Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA. Nat Chem Biol. 13(1):18–20.
   PubMed Web of Science ®Google Scholar
• Wilusz JE, Freier SM, Spector DL. 2008. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell. 135(5):919–932.
   PubMed Web of Science ®Google Scholar
• Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA. 2012. A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails. Genes Dev. 26(21):2392–2407.
   PubMed Web of Science ®Google Scholar
• Wiryaman T, Toor N. 2017. Structure determination of group II introns. Methods (San Diego, Calif. 125:10–15.
   PubMed Web of Science ®Google Scholar
• Woodson SA, Deras ML, Brenowitz M. 2001. Time-resolved hydroxyl radical footprinting of RNA with X-rays. In: Serge L Beaucage, et al., editors. Current protocols in nucleic acid chemistry. Hoboken (NJ): John Wiley & Sons, Inc, Chapter 11:Unit 11 16. DOI: 10.1002/0471142700.nc1106s06
   Google Scholar
• Wu L, Murat P, Matak-Vinkovic D, Murrell A, Balasubramanian S. 2013. Binding interactions between long noncoding RNA HOTAIR and PRC2 proteins. Biochemistry. 52(52):9519–9527.
   PubMed Web of Science ®Google Scholar
• Wutz A, Rasmussen TP, Jaenisch R. 2002. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet. 30(2):167–174.
   PubMed Web of Science ®Google Scholar
• Xu Y, Kaminaga K, Komiyama M. 2008. G-quadruplex formation by human telomeric repeats-containing RNA in Na + solution. J Am Chem Soc. 130(33):11179–11184.
   PubMed Web of Science ®Google Scholar
• Xue Z, Hennelly S, Doyle B, Gulati AA, Novikova IV, Sanbonmatsu KY, Boyer LA. 2016. A G-Rich motif in the lncRNA Braveheart interacts with a zinc-finger transcription factor to specify the cardiovascular lineage. Mol Cell. 64(1):37–50.
   PubMed Web of Science ®Google Scholar
• Yang D, Liu P, Wudeck EV, Giedroc DP, Leibowitz JL. 2015. SHAPE analysis of the RNA secondary structure of the Mouse Hepatitis Virus 5' untranslated region and N-terminal nsp1 coding sequences. Virology. 475:15–27.
   PubMed Web of Science ®Google Scholar
• Yang F, Zhang H, Mei Y, Wu M. 2014. Reciprocal regulation of HIF-1alpha and lincRNA-p21 modulates the Warburg effect. Mol Cell. 53(1):88–100.
   PubMed Web of Science ®Google Scholar
• Yang SY, Lejault P, Chevrier S, Boidot R, Robertson AG, Wong JMY, Monchaud D. 2018. Transcriptome-wide identification of transient RNA G-quadruplexes in human cells. Nat Commun. 9(1):4730.
   PubMedGoogle Scholar
• Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, et al. 2019. Computational design of three-dimensional RNA structure and function. Nat Nanotechnol. 14(9):866–873.
   PubMed Web of Science ®Google Scholar
• Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, et al. 2020. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature. 580(7801):147–150.
   PubMed Web of Science ®Google Scholar
• Yu J, Liu Z, Jiang W, Wang G, Mao C. 2015. De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism. Nat Commun. 6(1):5724.
   PubMedGoogle Scholar
• Zappulla DC, Cech TR. 2004. Yeast telomerase RNA: a flexible scaffold for protein subunits. Proc Natl Acad Sci USA. 101(27):10024–10029.
   PubMed Web of Science ®Google Scholar
• Zhang B, Gunawardane L, Niazi F, Jahanbani F, Chen X, Valadkhan S. 2014. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol Cell Biol. 34(12):2318–2329.
   PubMed Web of Science ®Google Scholar
• Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. 2019. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 A resolution. Nat Commun. 10(1):5511.
   PubMedGoogle Scholar
• Zhang X, Zhou Y, Mehta KR, Danila DC, Scolavino S, Johnson SR, Klibanski A. 2003. A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab. 88(11):5119–5126.
   PubMed Web of Science ®Google Scholar
• Zhao C, Rajashankar KR, Marcia M, Pyle AM. 2015. Crystal structure of group II intron domain 1 reveals a template for RNA assembly. Nat Chem Biol. 11(12):967–972.
   PubMed Web of Science ®Google Scholar
• Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. 2008. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science. 322(5902):750–756.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Wang J, Zeng C, Xiao Y. 2018. Evaluation of RNA secondary structure prediction for both base-pairing and topology. Biophys Rep. 4(3):123–132.
   Google Scholar
• Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL, Gejman R, Ansell PJ, Zhao J, Weng C, Klibanski A. 2007. Activation of p53 by MEG3 non-coding RNA. J Biol Chem. 282(34):24731–24742.
   PubMed Web of Science ®Google Scholar