Literature DB >> 25546503

Review toward all RNA structures, concisely.

Kevin M Weeks1.   

Abstract

Profound insights regarding nucleic acid structure and function can be gleaned from very simple, direct, and chemistry-based strategies. Our approach strives to incorporate the elegant physical insights that Don Crothers instilled in those who trained in his laboratory. Don emphasized the advantages of focusing on direct and concise experiments even when the final objective was to understand something complex-potentially including the large-scale architectures of the genomes of RNA viruses and the transcriptomes of cells. Here, the author reviews the intellectual path, and a few detours, that led to the development of the SHAPE-MaP and RING-MaP technologies for interrogating RNA structure and function at large scales. The author also argues that greater attention to creating direct, less inferential experiments will convert "omics" investigations into lasting and definitive contributions to our understanding of biological function.
© 2014 Wiley Periodicals, Inc.

Entities:  

Keywords:  RNA structure; chemical probing; concision; structure modeling

Mesh:

Substances:

Year:  2015        PMID: 25546503      PMCID: PMC4446244          DOI: 10.1002/bip.22601

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  30 in total

1.  RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Authors:  José Almeida Cruz; Marc-Frédérick Blanchet; Michal Boniecki; Janusz M Bujnicki; Shi-Jie Chen; Song Cao; Rhiju Das; Feng Ding; Nikolay V Dokholyan; Samuel Coulbourn Flores; Lili Huang; Christopher A Lavender; Véronique Lisi; François Major; Katarzyna Mikolajczak; Dinshaw J Patel; Anna Philips; Tomasz Puton; John Santalucia; Fredrick Sijenyi; Thomas Hermann; Kristian Rother; Magdalena Rother; Alexander Serganov; Marcin Skorupski; Tomasz Soltysinski; Parin Sripakdeevong; Irina Tuszynska; Kevin M Weeks; Christina Waldsich; Michael Wildauer; Neocles B Leontis; Eric Westhof
Journal:  RNA       Date:  2012-02-23       Impact factor: 4.942

2.  RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).

Authors:  Edward J Merino; Kevin A Wilkinson; Jennifer L Coughlan; Kevin M Weeks
Journal:  J Am Chem Soc       Date:  2005-03-30       Impact factor: 15.419

Review 3.  RNA structure prediction.

Authors:  D H Turner; N Sugimoto; S M Freier
Journal:  Annu Rev Biophys Biophys Chem       Date:  1988

4.  Ribosome RNA assembly intermediates visualized in living cells.

Authors:  Jennifer L McGinnis; Kevin M Weeks
Journal:  Biochemistry       Date:  2014-05-12       Impact factor: 3.162

5.  A guanosine-centric mechanism for RNA chaperone function.

Authors:  Jacob K Grohman; Robert J Gorelick; Colin R Lickwar; Jason D Lieb; Brian D Bower; Brent M Znosko; Kevin M Weeks
Journal:  Science       Date:  2013-03-07       Impact factor: 47.728

6.  Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA.

Authors:  Alexei V Kazantsev; Angelika A Krivenko; Norman R Pace
Journal:  RNA       Date:  2008-12-17       Impact factor: 4.942

7.  Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA.

Authors:  Costin M Gherghe; Zahra Shajani; Kevin A Wilkinson; Gabriele Varani; Kevin M Weeks
Journal:  J Am Chem Soc       Date:  2008-08-19       Impact factor: 15.419

8.  RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

Authors:  Greggory M Rice; Christopher W Leonard; Kevin M Weeks
Journal:  RNA       Date:  2014-04-17       Impact factor: 4.942

9.  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.

Authors: 
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

10.  RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).

Authors:  Nathan A Siegfried; Steven Busan; Greggory M Rice; Julie A E Nelson; Kevin M Weeks
Journal:  Nat Methods       Date:  2014-07-13       Impact factor: 28.547

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  17 in total

Review 1.  RNA Structural Differentiation: Opportunities with Pattern Recognition.

Authors:  Christopher S Eubanks; Amanda E Hargrove
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

2.  Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

Authors:  Matthew J Smola; Greggory M Rice; Steven Busan; Nathan A Siegfried; Kevin M Weeks
Journal:  Nat Protoc       Date:  2015-10-01       Impact factor: 13.491

3.  Small Molecule-Based Pattern Recognition To Classify RNA Structure.

Authors:  Christopher S Eubanks; Jordan E Forte; Gary J Kapral; Amanda E Hargrove
Journal:  J Am Chem Soc       Date:  2016-12-22       Impact factor: 15.419

4.  Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.

Authors:  Anthony M Mustoe; Steven Busan; Greggory M Rice; Christine E Hajdin; Brant K Peterson; Vera M Ruda; Neil Kubica; Razvan Nutiu; Jeremy L Baryza; Kevin M Weeks
Journal:  Cell       Date:  2018-03-15       Impact factor: 41.582

5.  Detection of RNA-Protein Interactions in Living Cells with SHAPE.

Authors:  Matthew J Smola; J Mauro Calabrese; Kevin M Weeks
Journal:  Biochemistry       Date:  2015-11-11       Impact factor: 3.162

Review 6.  SHAPE Directed Discovery of New Functions in Large RNAs.

Authors:  Kevin M Weeks
Journal:  Acc Chem Res       Date:  2021-05-07       Impact factor: 22.384

7.  Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.

Authors:  Thomas W Christy; Catherine A Giannetti; Gillian Houlihan; Matthew J Smola; Greggory M Rice; Jian Wang; Nikolay V Dokholyan; Alain Laederach; Philipp Holliger; Kevin M Weeks
Journal:  Biochemistry       Date:  2021-06-14       Impact factor: 3.321

8.  The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs.

Authors:  W-Matthias Leeder; Christin Voigt; Michael Brecht; H Ulrich Göringer
Journal:  Sci Rep       Date:  2016-01-19       Impact factor: 4.379

9.  Direct identification of base-paired RNA nucleotides by correlated chemical probing.

Authors:  Andrey Krokhotin; Anthony M Mustoe; Kevin M Weeks; Nikolay V Dokholyan
Journal:  RNA       Date:  2016-11-01       Impact factor: 4.942

Review 10.  Mechanisms of long noncoding RNA function in development and disease.

Authors:  Sandra U Schmitz; Phillip Grote; Bernhard G Herrmann
Journal:  Cell Mol Life Sci       Date:  2016-03-23       Impact factor: 9.261

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