Literature DB >> 27427309

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

Chase A Weidmann1, Anthony M Mustoe1, Kevin M Weeks2.   

Abstract

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID： 27427309      PMCID： PMC5002247          DOI： 10.1016/j.tibs.2016.07.001

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN： 0968-0004            Impact factor:   13.807


  10 in total

Review 1.  The emerging role of lncRNAs in cancer.

Authors:  Maite Huarte
Journal:  Nat Med       Date:  2015-11       Impact factor: 53.440

2.  Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.

Authors:  Grzegorz Kudla; Sander Granneman; Daniela Hahn; Jean D Beggs; David Tollervey
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-24       Impact factor: 11.205

Review 3.  The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

Authors:  Chun Kit Kwok; Yin Tang; Sarah M Assmann; Philip C Bevilacqua
Journal:  Trends Biochem Sci       Date:  2015-03-18       Impact factor: 13.807

Review 4.  The noncoding RNA revolution-trashing old rules to forge new ones.

Authors:  Thomas R Cech; Joan A Steitz
Journal:  Cell       Date:  2014-03-27       Impact factor: 41.582

5.  In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation.

Authors:  Jong Ghut Ashley Aw; Yang Shen; Andreas Wilm; Miao Sun; Xin Ni Lim; Kum-Loong Boon; Sidika Tapsin; Yun-Shen Chan; Cheng-Peow Tan; Adelene Y L Sim; Tong Zhang; Teodorus Theo Susanto; Zhiyan Fu; Niranjan Nagarajan; Yue Wan
Journal:  Mol Cell       Date:  2016-05-12       Impact factor: 17.970

6.  Global Mapping of Human RNA-RNA Interactions.

Authors:  Eesha Sharma; Tim Sterne-Weiler; Dave O'Hanlon; Benjamin J Blencowe
Journal:  Mol Cell       Date:  2016-05-12       Impact factor: 17.970

7.  RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

Authors:  Zhipeng Lu; Qiangfeng Cliff Zhang; Byron Lee; Ryan A Flynn; Martin A Smith; James T Robinson; Chen Davidovich; Anne R Gooding; Karen J Goodrich; John S Mattick; Jill P Mesirov; Thomas R Cech; Howard Y Chang
Journal:  Cell       Date:  2016-05-12       Impact factor: 41.582

8.  hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Authors:  Yoichiro Sugimoto; Alessandra Vigilante; Elodie Darbo; Alexandra Zirra; Cristina Militti; Andrea D'Ambrogio; Nicholas M Luscombe; Jernej Ule
Journal:  Nature       Date:  2015-03-18       Impact factor: 49.962

9.  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

10.  High-throughput determination of RNA structure by proximity ligation.

Authors:  Vijay Ramani; Ruolan Qiu; Jay Shendure
Journal:  Nat Biotechnol       Date:  2015-08-03       Impact factor: 54.908
  10 in total
  10 in total

1.  RNA base-pairing complexity in living cells visualized by correlated chemical probing.

Authors:  Anthony M Mustoe; Nicole N Lama; Patrick S Irving; Samuel W Olson; Kevin M Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2019-11-19       Impact factor: 11.205

2.  RNAnue: efficient data analysis for RNA-RNA interactomics.

Authors:  Richard A Schäfer; Björn Voß
Journal:  Nucleic Acids Res       Date:  2021-06-04       Impact factor: 16.971

3.  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

4.  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 5.  The Non-Coding Regulatory RNA Revolution in Archaea.

Authors:  Diego Rivera Gelsinger; Jocelyne DiRuggiero
Journal:  Genes (Basel)       Date:  2018-03-05       Impact factor: 4.096

6.  Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments.

Authors:  Alexander Borodavka; Eric C Dykeman; Waldemar Schrimpf; Don C Lamb
Journal:  Elife       Date:  2017-09-18       Impact factor: 8.140

Review 7.  RNA interactomics: recent advances and remaining challenges.

Authors:  Brigitte Schönberger; Christoph Schaal; Richard Schäfer; Björn Voß
Journal:  F1000Res       Date:  2018-11-20

8.  RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates.

Authors:  Simón Poblete; Anže Božič; Matej Kanduč; Rudolf Podgornik; Horacio V Guzman
Journal:  ACS Omega       Date:  2021-11-19

9.  Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper.

Authors:  Thomas W Christy; Catherine A Giannetti; Alain Laederach; Kevin M Weeks
Journal:  PLoS Comput Biol       Date:  2021-12-14       Impact factor: 4.779

Review 10.  RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity.

Authors:  Redmond P Smyth; Matteo Negroni; Andrew M Lever; Johnson Mak; Julia C Kenyon
Journal:  Front Immunol       Date:  2018-09-19       Impact factor: 7.561
  10 in total

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