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Literature DB >> 23178934

RNA SHAPE analysis in living cells.

Robert C Spitale¹, Pete Crisalli, Ryan A Flynn, Eduardo A Torre, Eric T Kool, Howard Y Chang.

Abstract

RNA structure has important roles in practically every facet of gene regulation, but the paucity of in vivo structural probes limits current understanding. Here we design, synthesize and demonstrate two new chemical probes that enable selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) in living cells. RNA structures in human, mouse, fly, yeast and bacterial cells are read out at single-nucleotide resolution, revealing tertiary contacts and RNA-protein interactions.

Entities: CellLine Chemical Disease Species

Mesh：

Substances：
RNA

Year: 2012 PMID： 23178934 PMCID： PMC3706714 DOI： 10.1038/nchembio.1131

Source DB: PubMed Journal: Nat Chem Biol ISSN： 1552-4450 Impact factor: 15.040

25 in total

1. 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

2. Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast.

Authors: Elisabeth M Mahen; Jason W Harger; Elise M Calderon; Martha J Fedor
Journal: Mol Cell Date: 2005-07-01 Impact factor: 17.970

3. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling.

Authors: C Brunel; P Romby; E Westhof; C Ehresmann; B Ehresmann
Journal: J Mol Biol Date: 1991-09-05 Impact factor: 5.469

4. Accurate SHAPE-directed RNA structure determination.

Authors: Katherine E Deigan; Tian W Li; David H Mathews; Kevin M Weeks
Journal: Proc Natl Acad Sci U S A Date: 2008-12-24 Impact factor: 11.205

5. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

6. In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis.

Authors: D Luo; C Condon; M Grunberg-Manago; H Putzer
Journal: Nucleic Acids Res Date: 1998-12-01 Impact factor: 16.971

7. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

Authors: Kevin A Wilkinson; Robert J Gorelick; Suzy M Vasa; Nicolas Guex; Alan Rein; David H Mathews; Morgan C Giddings; Kevin M Weeks
Journal: PLoS Biol Date: 2008-04-29 Impact factor: 8.029

8. Coding-sequence determinants of gene expression in Escherichia coli.

Authors: Grzegorz Kudla; Andrew W Murray; David Tollervey; Joshua B Plotkin
Journal: Science Date: 2009-04-10 Impact factor: 47.728

9. DMS footprinting of structured RNAs and RNA-protein complexes.

Authors: Pilar Tijerina; Sabine Mohr; Rick Russell
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

10. 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

178 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. Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.

Authors: Griffin M Schroeder; Debapratim Dutta; Chapin E Cavender; Jermaine L Jenkins; Elizabeth M Pritchett; Cameron D Baker; John M Ashton; David H Mathews; Joseph E Wedekind
Journal: Nucleic Acids Res Date: 2020-08-20 Impact factor: 16.971

3. 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

RNA SHAPE analysis in living cells.

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

2. Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast.

3. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling.

4. Accurate SHAPE-directed RNA structure determination.

5. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

6. In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis.

7. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

8. Coding-sequence determinants of gene expression in Escherichia coli.

9. DMS footprinting of structured RNAs and RNA-protein complexes.

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

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

2. Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.

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

4. Finding function in mystery transcripts.

Review 5. Probing dimensionality beyond the linear sequence of mRNA.

Review 6. Small molecule targeting of RNA structures in neurological disorders.

7. Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE.

8. In-cell RNA structure probing with SHAPE-MaP.

Review 9. Long non-coding RNAs: modulators of nuclear structure and function.

10. The cellular environment stabilizes adenine riboswitch RNA structure.