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For: Siegfried NA, Busan S, Rice GM, Nelson JA, Weeks KM. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods 2014;11:959-65. [PMID: 25028896 PMCID: PMC4259394 DOI: 10.1038/nmeth.3029] [Citation(s) in RCA: 444] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/08/2014] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
351
Antzin-Anduetza I, Mahiet C, Granger LA, Odendall C, Swanson CM. Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication. Retrovirology 2017;14:49. [PMID: 29121951 PMCID: PMC5679385 DOI: 10.1186/s12977-017-0374-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022]  Open
352
Liu Y, Chen J, Nikolaitchik OA, Desimmie BA, Busan S, Pathak VK, Weeks KM, Hu WS. The roles of five conserved lentiviral RNA structures in HIV-1 replication. Virology 2017;514:1-8. [PMID: 29128752 DOI: 10.1016/j.virol.2017.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 11/16/2022]
353
Sztuba-Solinska J, Rausch JW, Smith R, Miller JT, Whitby D, Le Grice SFJ. Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins. Nucleic Acids Res 2017;45:6805-6821. [PMID: 28383682 PMCID: PMC5499733 DOI: 10.1093/nar/gkx241] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/30/2017] [Indexed: 01/04/2023]  Open
354
An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc Natl Acad Sci U S A 2017;114:E10244-E10253. [PMID: 29109288 PMCID: PMC5703279 DOI: 10.1073/pnas.1706539114] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
355
Lei Z, Yi C. A Radiolabeling-Free, qPCR-Based Method for Locus-Specific Pseudouridine Detection. Angew Chem Int Ed Engl 2017;56:14878-14882. [DOI: 10.1002/anie.201708276] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 12/19/2022]
356
Deforges J, de Breyne S, Ameur M, Ulryck N, Chamond N, Saaidi A, Ponty Y, Ohlmann T, Sargueil B. Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame. Nucleic Acids Res 2017;45:7382-7400. [PMID: 28449096 PMCID: PMC5499600 DOI: 10.1093/nar/gkx303] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023]  Open
357
Piao M, Sun L, Zhang QC. RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. GENOMICS PROTEOMICS & BIOINFORMATICS 2017;15:267-278. [PMID: 29031843 PMCID: PMC5673676 DOI: 10.1016/j.gpb.2017.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/09/2017] [Accepted: 05/27/2017] [Indexed: 01/07/2023]
358
Alenko A, Fleming AM, Burrows CJ. Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers. Biochemistry 2017;56:5053-5064. [PMID: 28845978 DOI: 10.1021/acs.biochem.7b00730] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
359
Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA. Biochemistry 2017;56:4713-4721. [PMID: 28820243 PMCID: PMC5648349 DOI: 10.1021/acs.biochem.7b00323] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
360
Huber RG, Marzinek JK, Holdbrook DA, Bond PJ. Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;128:121-132. [DOI: 10.1016/j.pbiomolbio.2016.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022]
361
RNA structure inference through chemical mapping after accidental or intentional mutations. Proc Natl Acad Sci U S A 2017;114:9876-9881. [PMID: 28851837 DOI: 10.1073/pnas.1619897114] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
362
Ball CB, Solem AC, Meganck RM, Laederach A, Ramos SBV. Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA. RNA (NEW YORK, N.Y.) 2017;23:1209-1223. [PMID: 28455422 PMCID: PMC5513066 DOI: 10.1261/rna.060467.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
363
Schlick T, Pyle AM. Opportunities and Challenges in RNA Structural Modeling and Design. Biophys J 2017;113:225-234. [PMID: 28162235 PMCID: PMC5529161 DOI: 10.1016/j.bpj.2016.12.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/27/2023]  Open
364
Dawn of the in vivo RNA structurome and interactome. Biochem Soc Trans 2017;44:1395-1410. [PMID: 27911722 DOI: 10.1042/bst20160075] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/19/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
365
Busan S, Weeks KM. Visualization of RNA structure models within the Integrative Genomics Viewer. RNA (NEW YORK, N.Y.) 2017;23:1012-1018. [PMID: 28428329 PMCID: PMC5473135 DOI: 10.1261/rna.060194.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
366
Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A. Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J 2017. [PMID: 28625696 PMCID: PMC5529173 DOI: 10.1016/j.bpj.2017.05.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
367
Shi J, Li X, Dong M, Graham M, Yadav N, Liang C. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. PLoS One 2017;12:e0179040. [PMID: 28582416 PMCID: PMC5459502 DOI: 10.1371/journal.pone.0179040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/23/2017] [Indexed: 11/19/2022]  Open
368
Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017;45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
369
McClary B, Zinshteyn B, Meyer M, Jouanneau M, Pellegrino S, Yusupova G, Schuller A, Reyes JCP, Lu J, Guo Z, Ayinde S, Luo C, Dang Y, Romo D, Yusupov M, Green R, Liu JO. Inhibition of Eukaryotic Translation by the Antitumor Natural Product Agelastatin A. Cell Chem Biol 2017;24:605-613.e5. [PMID: 28457705 PMCID: PMC5562292 DOI: 10.1016/j.chembiol.2017.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/09/2017] [Accepted: 04/06/2017] [Indexed: 01/10/2023]
370
Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst 2017;4:568-574.e7. [PMID: 28501650 DOI: 10.1016/j.cels.2017.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/19/2016] [Accepted: 04/13/2017] [Indexed: 11/19/2022]
371
Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell 2017;167:1610-1622.e15. [PMID: 27912064 DOI: 10.1016/j.cell.2016.11.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/08/2016] [Accepted: 11/11/2016] [Indexed: 11/23/2022]
372
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (NEW YORK, N.Y.) 2017;23:655-672. [PMID: 28138060 PMCID: PMC5393176 DOI: 10.1261/rna.060368.116] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 01/26/2017] [Indexed: 05/21/2023]
373
Larman BC, Dethoff EA, Weeks KM. Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States. Biochemistry 2017;56:2175-2183. [PMID: 28332826 DOI: 10.1021/acs.biochem.6b01166] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
374
RNA structure through multidimensional chemical mapping. Q Rev Biophys 2017;49:e7. [PMID: 27266715 DOI: 10.1017/s0033583516000020] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
375
Chan D, Feng C, Spitale RC. Measuring RNA structure transcriptome-wide with icSHAPE. Methods 2017;120:85-90. [PMID: 28336307 DOI: 10.1016/j.ymeth.2017.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/26/2017] [Accepted: 02/27/2017] [Indexed: 11/17/2022]  Open
376
Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017;5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
377
Portoso M, Ragazzini R, Brenčič Ž, Moiani A, Michaud A, Vassilev I, Wassef M, Servant N, Sargueil B, Margueron R. PRC2 is dispensable for HOTAIR-mediated transcriptional repression. EMBO J 2017;36:981-994. [PMID: 28167697 PMCID: PMC5391141 DOI: 10.15252/embj.201695335] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022]  Open
378
Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA (NEW YORK, N.Y.) 2017;23:169-174. [PMID: 27879433 PMCID: PMC5238792 DOI: 10.1261/rna.058784.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/20/2016] [Indexed: 05/10/2023]
379
Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. Small Molecule-Based Pattern Recognition To Classify RNA Structure. J Am Chem Soc 2017;139:409-416. [PMID: 28004925 PMCID: PMC5465965 DOI: 10.1021/jacs.6b11087] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
380
Krokhotin A, Mustoe AM, Weeks KM, Dokholyan NV. Direct identification of base-paired RNA nucleotides by correlated chemical probing. RNA (NEW YORK, N.Y.) 2017;23:6-13. [PMID: 27803152 PMCID: PMC5159650 DOI: 10.1261/rna.058586.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/28/2016] [Indexed: 05/04/2023]
381
Zanini F, Puller V, Brodin J, Albert J, Neher RA. In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evol 2017;3:vex003. [PMID: 28458914 PMCID: PMC5399928 DOI: 10.1093/ve/vex003] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
382
Incarnato D, Oliviero S. The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications. Trends Biotechnol 2016;35:318-333. [PMID: 27988057 DOI: 10.1016/j.tibtech.2016.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
383
Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB. Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat Struct Mol Biol 2016;23:1124-1131. [PMID: 27798597 PMCID: PMC5497173 DOI: 10.1038/nsmb.3316] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/05/2016] [Indexed: 12/19/2022]
384
Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments. Nat Methods 2016;14:83-89. [DOI: 10.1038/nmeth.4068] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 10/03/2016] [Indexed: 12/20/2022]
385
DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods 2016;14:75-82. [PMID: 27819661 DOI: 10.1038/nmeth.4057] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/29/2016] [Indexed: 12/25/2022]
386
Thomas EM, Testa SM. The colorimetric determination of selectively cleaved adenosines and guanosines in DNA oligomers using bicinchoninic acid and copper. J Biol Inorg Chem 2016;22:31-46. [PMID: 27807667 DOI: 10.1007/s00775-016-1405-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
387
Cross- and Co-Packaging of Retroviral RNAs and Their Consequences. Viruses 2016;8:v8100276. [PMID: 27727192 PMCID: PMC5086612 DOI: 10.3390/v8100276] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 12/23/2022]  Open
388
Song J, Perreault JP, Topisirovic I, Richard S. RNA G-quadruplexes and their potential regulatory roles in translation. ACTA ACUST UNITED AC 2016;4:e1244031. [PMID: 28090421 PMCID: PMC5173311 DOI: 10.1080/21690731.2016.1244031] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
389
Mongkolsiriwattana C, Zhou JS, Ng JCK. A 3'-end structure in RNA2 of a crinivirus is essential for viral RNA synthesis and contributes to replication-associated translation activity. Sci Rep 2016;6:34482. [PMID: 27694962 PMCID: PMC5046102 DOI: 10.1038/srep34482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/12/2016] [Indexed: 01/31/2023]  Open
390
Bevilacqua PC, Ritchey LE, Su Z, Assmann SM. Genome-Wide Analysis of RNA Secondary Structure. Annu Rev Genet 2016;50:235-266. [PMID: 27648642 DOI: 10.1146/annurev-genet-120215-035034] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
391
The Life-Cycle of the HIV-1 Gag-RNA Complex. Viruses 2016;8:v8090248. [PMID: 27626439 PMCID: PMC5035962 DOI: 10.3390/v8090248] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022]  Open
392
SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc Natl Acad Sci U S A 2016;113:10322-7. [PMID: 27578869 DOI: 10.1073/pnas.1600008113] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
393
Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF. J Bacteriol 2016;198:2458-69. [PMID: 27381913 DOI: 10.1128/jb.00343-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/27/2016] [Indexed: 01/13/2023]  Open
394
Crawford DW, Blakeley BD, Chen PH, Sherpa C, Le Grice SF, Laird-Offringa IA, McNaughton BR. An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chem Biol 2016;11:2206-15. [PMID: 27253715 DOI: 10.1021/acschembio.6b00145] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
395
Deng F, Ledda M, Vaziri S, Aviran S. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA (NEW YORK, N.Y.) 2016;22:1109-1119. [PMID: 27251549 PMCID: PMC4931104 DOI: 10.1261/rna.055756.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
396
Weidmann CA, Mustoe AM, Weeks KM. Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox. Trends Biochem Sci 2016;41:734-736. [PMID: 27427309 DOI: 10.1016/j.tibs.2016.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/01/2016] [Indexed: 11/18/2022]
397
Kutchko KM, Laederach A. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016;8. [PMID: 27396578 PMCID: PMC5179297 DOI: 10.1002/wrna.1374] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
398
Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res 2016;25:1456-65. [PMID: 26430155 PMCID: PMC4579330 DOI: 10.1101/gr.191122.115] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
399
Huang L, Wang J, Lilley DMJ. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function. Nucleic Acids Res 2016;44:5390-8. [PMID: 27016741 PMCID: PMC4914095 DOI: 10.1093/nar/gkw201] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/08/2016] [Accepted: 03/14/2016] [Indexed: 11/20/2022]  Open
400
Kalloush RM, Vivet-Boudou V, Ali LM, Mustafa F, Marquet R, Rizvi TA. Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences. RNA (NEW YORK, N.Y.) 2016;22:905-919. [PMID: 27095024 PMCID: PMC4878616 DOI: 10.1261/rna.055731.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
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