Literature DB >> 31182864

The roles of structural dynamics in the cellular functions of RNAs.

Laura R Ganser1, Megan L Kelly1, Daniel Herschlag2,3,4, Hashim M Al-Hashimi5,6.   

Abstract

RNAs fold into 3D structures that range from simple helical elements to complex tertiary structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory RNAs depend on how their 3D structure changes in response to a diverse array of cellular conditions. In this Review, we examine how the structural characterization of RNA as dynamic ensembles of conformations, which form with different probabilities and at different timescales, is improving our understanding of RNA function in cells. We discuss the mechanisms of gene regulation by microRNAs, riboswitches, ribozymes, post-transcriptional RNA modifications and RNA-binding proteins, and how the cellular environment and processes such as liquid-liquid phase separation may affect RNA folding and activity. The emerging RNA-ensemble-function paradigm is changing our perspective and understanding of RNA regulation, from in vitro to in vivo and from descriptive to predictive.

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Year:  2019        PMID: 31182864      PMCID: PMC7656661          DOI: 10.1038/s41580-019-0136-0

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  151 in total

Review 1.  How RNA folds.

Authors:  I Tinoco; C Bustamante
Journal:  J Mol Biol       Date:  1999-10-22       Impact factor: 5.469

2.  Visualizing spatially correlated dynamics that directs RNA conformational transitions.

Authors:  Qi Zhang; Andrew C Stelzer; Charles K Fisher; Hashim M Al-Hashimi
Journal:  Nature       Date:  2007-12-20       Impact factor: 49.962

3.  NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.

Authors:  Christina Helmling; Anna Wacker; Michael T Wolfinger; Ivo L Hofacker; Martin Hengesbach; Boris Fürtig; Harald Schwalbe
Journal:  J Am Chem Soc       Date:  2017-02-13       Impact factor: 15.419

4.  Invisible RNA state dynamically couples distant motifs.

Authors:  Janghyun Lee; Elizabeth A Dethoff; Hashim M Al-Hashimi
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-16       Impact factor: 11.205

5.  Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Authors:  Jean-Denis Beaudoin; Eva Maria Novoa; Charles E Vejnar; Valeria Yartseva; Carter M Takacs; Manolis Kellis; Antonio J Giraldez
Journal:  Nat Struct Mol Biol       Date:  2018-07-30       Impact factor: 15.369

6.  Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit.

Authors:  Ambadas B Rode; Tamaki Endoh; Naoki Sugimoto
Journal:  Angew Chem Int Ed Engl       Date:  2018-04-27       Impact factor: 15.336

7.  A toxic RNA catalyzes the in cellulo synthesis of its own inhibitor.

Authors:  Suzanne G Rzuczek; HaJeung Park; Matthew D Disney
Journal:  Angew Chem Int Ed Engl       Date:  2014-08-27       Impact factor: 15.336

8.  Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.

Authors:  Dominic Lambert; David E Draper
Journal:  J Mol Biol       Date:  2007-05-05       Impact factor: 5.469

9.  Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation.

Authors:  Hannah Steinert; Florian Sochor; Anna Wacker; Janina Buck; Christina Helmling; Fabian Hiller; Sara Keyhani; Jonas Noeske; Steffen Grimm; Martin M Rudolph; Heiko Keller; Rachel Anne Mooney; Robert Landick; Beatrix Suess; Boris Fürtig; Jens Wöhnert; Harald Schwalbe
Journal:  Elife       Date:  2017-05-25       Impact factor: 8.140

10.  Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.

Authors:  Hua Li; Sharon Aviran
Journal:  Nat Commun       Date:  2018-02-09       Impact factor: 14.919

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  80 in total

1.  Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding.

Authors:  Olivier Duss; Galina A Stepanyuk; Joseph D Puglisi; James R Williamson
Journal:  Cell       Date:  2019-11-21       Impact factor: 41.582

Review 2.  RNA contributions to the form and function of biomolecular condensates.

Authors:  Christine Roden; Amy S Gladfelter
Journal:  Nat Rev Mol Cell Biol       Date:  2020-07-06       Impact factor: 94.444

3.  mRNA structural dynamics shape Argonaute-target interactions.

Authors:  Suzan Ruijtenberg; Stijn Sonneveld; Tao Ju Cui; Ive Logister; Dion de Steenwinkel; Yao Xiao; Ian J MacRae; Chirlmin Joo; Marvin E Tanenbaum
Journal:  Nat Struct Mol Biol       Date:  2020-07-13       Impact factor: 15.369

4.  Small molecule-RNA targeting: starting with the fundamentals.

Authors:  Amanda E Hargrove
Journal:  Chem Commun (Camb)       Date:  2020-11-26       Impact factor: 6.222

5.  Visualizing a protonated RNA state that modulates microRNA-21 maturation.

Authors:  Jared T Baisden; Joshua A Boyer; Bo Zhao; Scott M Hammond; Qi Zhang
Journal:  Nat Chem Biol       Date:  2020-10-26       Impact factor: 15.040

6.  Visualizing a viral genome with contrast variation small angle X-ray scattering.

Authors:  Josue San Emeterio; Lois Pollack
Journal:  J Biol Chem       Date:  2020-09-10       Impact factor: 5.157

7.  Probing RNA Conformational Equilibria within the Functional Cellular Context.

Authors:  Laura R Ganser; Chia-Chieh Chu; Hal P Bogerd; Megan L Kelly; Bryan R Cullen; Hashim M Al-Hashimi
Journal:  Cell Rep       Date:  2020-02-25       Impact factor: 9.423

8.  More or less - the same? mRNA fluctuations are balanced during translation.

Authors:  Itamar Kozlovski; Reuven Agami
Journal:  EMBO J       Date:  2019-10-22       Impact factor: 11.598

9.  Exposing Hidden High-Affinity RNA Conformational States.

Authors:  Nicole I Orlovsky; Hashim M Al-Hashimi; Terrence G Oas
Journal:  J Am Chem Soc       Date:  2019-12-31       Impact factor: 15.419

10.  Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy.

Authors:  Bo Zhao; Jared T Baisden; Qi Zhang
Journal:  J Magn Reson       Date:  2019-11-11       Impact factor: 2.229

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