Literature DB >> 21045541

RNA folding in living cells.

Georgeta Zemora1, Christina Waldsich.   

Abstract

RNA folding is the most essential process underlying RNA function. While significant progress has been made in understanding the forces driving RNA folding in vitro, exploring the rules governing intracellular RNA structure formation is still in its infancy. The cellular environment hosts a great diversity of factors that potentially influence RNA folding in vivo. For example, the nature of transcription and translation is known to shape the folding landscape of RNA molecules. Trans-acting factors such as proteins, RNAs and metabolites, among others, are also able to modulate the structure and thus the fate of an RNA. Here we summarize the ongoing efforts to uncover how RNA folds in living cells.

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Year:  2010        PMID: 21045541      PMCID: PMC3073324          DOI: 10.4161/rna.7.6.13554

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  141 in total

1.  A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence.

Authors:  Amy Diegelman-Parente; Philip C Bevilacqua
Journal:  J Mol Biol       Date:  2002-11-15       Impact factor: 5.469

Review 2.  Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions.

Authors:  Olga Fedorova; Linhui Julie Su; Anna Marie Pyle
Journal:  Methods       Date:  2002-11       Impact factor: 3.608

3.  Effect of transcription on folding of the Tetrahymena ribozyme.

Authors:  Susan L Heilman-Miller; Sarah A Woodson
Journal:  RNA       Date:  2003-06       Impact factor: 4.942

4.  Monitoring intermediate folding states of the td group I intron in vivo.

Authors:  Christina Waldsich; Benoît Masquida; Eric Westhof; Renée Schroeder
Journal:  EMBO J       Date:  2002-10-01       Impact factor: 11.598

5.  RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo.

Authors:  Christina Waldsich; Rupert Grossberger; Renée Schroeder
Journal:  Genes Dev       Date:  2002-09-01       Impact factor: 11.361

6.  An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes.

Authors:  Jörgen Johansson; Pierre Mandin; Adriana Renzoni; Claude Chiaruttini; Mathias Springer; Pascale Cossart
Journal:  Cell       Date:  2002-09-06       Impact factor: 41.582

Review 7.  RNA folding in vivo.

Authors:  Renée Schroeder; Rupert Grossberger; Andrea Pichler; Christina Waldsich
Journal:  Curr Opin Struct Biol       Date:  2002-06       Impact factor: 6.809

8.  Perturbed folding kinetics of circularly permuted RNAs with altered topology.

Authors:  Susan L Heilman-Miller; Sarah A Woodson
Journal:  J Mol Biol       Date:  2003-04-25       Impact factor: 5.469

Review 9.  On the importance of being co-transcriptional.

Authors:  Karla M Neugebauer
Journal:  J Cell Sci       Date:  2002-10-15       Impact factor: 5.285

Review 10.  The catalytic mechanism of the hairpin ribozyme.

Authors:  M J Fedor
Journal:  Biochem Soc Trans       Date:  2002-11       Impact factor: 5.407

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  25 in total

1.  Understanding the kinetic mechanism of RNA single base pair formation.

Authors:  Xiaojun Xu; Tao Yu; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-22       Impact factor: 11.205

Review 2.  Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs.

Authors:  Thomas C Roberts; Kevin V Morris; Marc S Weinberg
Journal:  Epigenetics       Date:  2013-10-22       Impact factor: 4.528

3.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Authors:  Yiliang Ding; Yin Tang; Chun Kit Kwok; Yu Zhang; Philip C Bevilacqua; Sarah M Assmann
Journal:  Nature       Date:  2013-11-24       Impact factor: 49.962

4.  ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo.

Authors:  Jeffrey P Potratz; Mark Del Campo; Rachel Z Wolf; Alan M Lambowitz; Rick Russell
Journal:  J Mol Biol       Date:  2011-06-07       Impact factor: 5.469

Review 5.  Understanding the transcriptome through RNA structure.

Authors:  Yue Wan; Michael Kertesz; Robert C Spitale; Eran Segal; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2011-08-18       Impact factor: 53.242

6.  RNA catalysis as a probe for chaperone activity of DEAD-box helicases.

Authors:  Jeffrey P Potratz; Rick Russell
Journal:  Methods Enzymol       Date:  2012       Impact factor: 1.600

Review 7.  Progress and challenges for chemical probing of RNA structure inside living cells.

Authors:  Miles Kubota; Catherine Tran; Robert C Spitale
Journal:  Nat Chem Biol       Date:  2015-11-17       Impact factor: 15.040

8.  The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.

Authors:  David Mitchell; Inga Jarmoskaite; Nikhil Seval; Soenke Seifert; Rick Russell
Journal:  J Mol Biol       Date:  2013-05-20       Impact factor: 5.469

9.  The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly.

Authors:  Wai Kit Ma; Sara C Cloutier; Elizabeth J Tran
Journal:  J Mol Biol       Date:  2013-05-28       Impact factor: 5.469

Review 10.  Structure and mechanism of purine-binding riboswitches.

Authors:  Robert T Batey
Journal:  Q Rev Biophys       Date:  2012-07-31       Impact factor: 5.318

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