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For: Lai D, Proctor JR, Meyer IM. On the importance of cotranscriptional RNA structure formation. RNA 2013;19:1461-1473. [PMID: 24131802 PMCID: PMC3851714 DOI: 10.1261/rna.037390.112] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Number Cited by Other Article(s)
101
Liu SR, Hu CG, Zhang JZ. Regulatory effects of cotranscriptional RNA structure formation and transitions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016;7:562-74. [PMID: 27028291 DOI: 10.1002/wrna.1350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
102
McKeague M, Wong RS, Smolke CD. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res 2016;44:2987-99. [PMID: 26969733 PMCID: PMC4838379 DOI: 10.1093/nar/gkw151] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022]  Open
103
Endoh T, Rode AB, Takahashi S, Kataoka Y, Kuwahara M, Sugimoto N. Real-Time Monitoring of G-Quadruplex Formation during Transcription. Anal Chem 2016;88:1984-9. [PMID: 26810457 DOI: 10.1021/acs.analchem.5b04396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
104
Rinaldi AJ, Lund PE, Blanco MR, Walter NG. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat Commun 2016;7:8976. [PMID: 26781350 PMCID: PMC4735710 DOI: 10.1038/ncomms9976] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023]  Open
105
Cugusi S, Li Y, Jin P, Lucchesi JC. The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts. PLoS Genet 2016;12:e1005761. [PMID: 26752049 PMCID: PMC4710571 DOI: 10.1371/journal.pgen.1005761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/02/2015] [Indexed: 12/28/2022]  Open
106
Björk P, Wieslander L. The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes. Annu Rev Biochem 2015;84:65-92. [PMID: 26034888 DOI: 10.1146/annurev-biochem-060614-034150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
107
Zhu JYA, Meyer IM. Four RNA families with functional transient structures. RNA Biol 2015;12:5-20. [PMID: 25751035 PMCID: PMC4615214 DOI: 10.1080/15476286.2015.1008373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]  Open
108
Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015;33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
109
Silencing efficacy prediction: a retrospective study on target mRNA features. Biosci Rep 2015;35:BSR20140147. [PMID: 25702798 PMCID: PMC4381284 DOI: 10.1042/bsr20140147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
110
Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. Characterizing RNA Excited States Using NMR Relaxation Dispersion. Methods Enzymol 2015;558:39-73. [PMID: 26068737 DOI: 10.1016/bs.mie.2015.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
111
Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015;114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
112
Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM. Native Purification and Analysis of Long RNAs. Methods Enzymol 2015;558:3-37. [PMID: 26068736 PMCID: PMC4477701 DOI: 10.1016/bs.mie.2015.01.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
113
Senter E, Clote P. Fast, approximate kinetics of RNA folding. J Comput Biol 2015;22:124-44. [PMID: 25684201 DOI: 10.1089/cmb.2014.0193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
114
Badelt S, Hammer S, Flamm C, Hofacker IL. Thermodynamic and kinetic folding of riboswitches. Methods Enzymol 2015;553:193-213. [PMID: 25726466 DOI: 10.1016/bs.mie.2014.10.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
115
Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Res 2015;43:1859-68. [PMID: 25618847 PMCID: PMC4330374 DOI: 10.1093/nar/gkv010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
116
Pyle AM. Looking at LncRNAs with the ribozyme toolkit. Mol Cell 2014;56:13-7. [PMID: 25280101 DOI: 10.1016/j.molcel.2014.08.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
117
Sowa SW, Vazquez-Anderson J, Clark CA, De La Peña R, Dunn K, Fung EK, Khoury MJ, Contreras LM. Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence. Nucleic Acids Res 2014;43:e13. [PMID: 25416800 PMCID: PMC4333371 DOI: 10.1093/nar/gku1191] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
118
Schroeder SJ. Probing viral genomic structure: alternative viewpoints and alternative structures for satellite tobacco mosaic virus RNA. Biochemistry 2014;53:6728-37. [PMID: 25320869 DOI: 10.1021/bi501051k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
119
Theil EC. IRE mRNA riboregulators use metabolic iron (Fe(2+)) to control mRNA activity and iron chemistry in animals. Metallomics 2014;7:15-24. [PMID: 25209685 DOI: 10.1039/c4mt00136b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
120
Closed for business: exit-channel coupling to active site conformation in bacterial RNA polymerase. Nat Struct Mol Biol 2014;21:741-2. [DOI: 10.1038/nsmb.2883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
121
Hein PP, Kolb KE, Windgassen T, Bellecourt MJ, Darst SA, Mooney RA, Landick R. RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement. Nat Struct Mol Biol 2014;21:794-802. [PMID: 25108353 PMCID: PMC4156911 DOI: 10.1038/nsmb.2867] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022]
122
Björk P, Wieslander L. Mechanisms of mRNA export. Semin Cell Dev Biol 2014;32:47-54. [PMID: 24813364 DOI: 10.1016/j.semcdb.2014.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 02/02/2023]
123
Lai D, Meyer IM. e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation. Nucleic Acids Res 2014;42:W373-6. [PMID: 24810851 PMCID: PMC4086097 DOI: 10.1093/nar/gku292] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
124
Krajewski SS, Narberhaus F. Temperature-driven differential gene expression by RNA thermosensors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014;1839:978-988. [PMID: 24657524 DOI: 10.1016/j.bbagrm.2014.03.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/28/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
125
Clabbers MTB, Olsthoorn RCL, Gultyaev AP. Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region. ACTA ACUST UNITED AC 2014;30:1800-4. [PMID: 24590440 DOI: 10.1093/bioinformatics/btu122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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