Literature DB >> 26923056

Decoding the RNA structurome.

Zhipeng Lu1, Howard Y Chang2.   

Abstract

Structures of RNA molecules are essential for their architectural, regulatory, and catalytic functions. Recent advances in high throughput sequencing enabled the development of methods for probing RNA structures on a transcriptome-wide scale-termed the RNA structurome. Here we review the state-of-the-art technologies for probing the RNA structurome, and highlight insights gained from these studies. We also point out the limits of current methods and discuss potential directions for future improvements.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 26923056      PMCID: PMC4785074          DOI: 10.1016/j.sbi.2016.01.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  34 in total

1.  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

Review 2.  Cytotopic localization by long noncoding RNAs.

Authors:  Pedro J Batista; Howard Y Chang
Journal:  Curr Opin Cell Biol       Date:  2012-12-29       Impact factor: 8.382

3.  Understanding the errors of SHAPE-directed RNA structure modeling.

Authors:  Wipapat Kladwang; Christopher C VanLang; Pablo Cordero; Rhiju Das
Journal:  Biochemistry       Date:  2011-08-25       Impact factor: 3.162

4.  RNA SHAPE analysis in living cells.

Authors:  Robert C Spitale; Pete Crisalli; Ryan A Flynn; Eduardo A Torre; Eric T Kool; Howard Y Chang
Journal:  Nat Chem Biol       Date:  2012-11-25       Impact factor: 15.040

Review 5.  DEAD box RNA helicase functions in cancer.

Authors:  Frances V Fuller-Pace
Journal:  RNA Biol       Date:  2013-01-01       Impact factor: 4.652

6.  Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.

Authors:  Aleksandra Helwak; Grzegorz Kudla; Tatiana Dudnakova; David Tollervey
Journal:  Cell       Date:  2013-04-25       Impact factor: 41.582

7.  IRES-mediated translation of cellular messenger RNA operates in eIF2α- independent manner during stress.

Authors:  Nehal Thakor; Martin Holcik
Journal:  Nucleic Acids Res       Date:  2011-09-14       Impact factor: 16.971

8.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Authors:  Silvi Rouskin; Meghan Zubradt; Stefan Washietl; Manolis Kellis; Jonathan S Weissman
Journal:  Nature       Date:  2013-12-15       Impact factor: 49.962

9.  Mod-seq: high-throughput sequencing for chemical probing of RNA structure.

Authors:  Jason Talkish; Gemma May; Yizhu Lin; John L Woolford; C Joel McManus
Journal:  RNA       Date:  2014-03-24       Impact factor: 4.942

10.  Landscape and variation of RNA secondary structure across the human transcriptome.

Authors:  Yue Wan; Kun Qu; Qiangfeng Cliff Zhang; Ryan A Flynn; Ohad Manor; Zhengqing Ouyang; Jiajing Zhang; Robert C Spitale; Michael P Snyder; Eran Segal; Howard Y Chang
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

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  36 in total

Review 1.  The RNA Base-Pairing Problem and Base-Pairing Solutions.

Authors:  Zhipeng Lu; Howard Y Chang
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-12-03       Impact factor: 10.005

2.  Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.

Authors:  Krishna Choudhary; Fei Deng; Sharon Aviran
Journal:  Quant Biol       Date:  2017-03-30

3.  SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.

Authors:  Krishna Choudhary; Luyao Ruan; Fei Deng; Nathan Shih; Sharon Aviran
Journal:  Bioinformatics       Date:  2017-02-01       Impact factor: 6.937

4.  Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine.

Authors:  Matthew D Disney
Journal:  J Am Chem Soc       Date:  2019-04-19       Impact factor: 15.419

5.  Macrocyclization of a Ligand Targeting a Toxic RNA Dramatically Improves Potency.

Authors:  Raphael I Benhamou; Simon Vezina-Dawod; Shruti Choudhary; Kye Won Wang; Samantha M Meyer; Ilyas Yildirim; Matthew D Disney
Journal:  Chembiochem       Date:  2020-08-26       Impact factor: 3.164

6.  Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.

Authors:  May Daher; Julia R Widom; Wendy Tay; Nils G Walter
Journal:  J Mol Biol       Date:  2017-11-08       Impact factor: 5.469

7.  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

Review 8.  Mechanistic insights in X-chromosome inactivation.

Authors:  Zhipeng Lu; Ava C Carter; Howard Y Chang
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-11-05       Impact factor: 6.237

9.  PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution.

Authors:  Zhipeng Lu; Jing Gong; Qiangfeng Cliff Zhang
Journal:  Methods Mol Biol       Date:  2018

10.  Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

Authors:  Kyle E Watters; Krishna Choudhary; Sharon Aviran; Julius B Lucks; Keith L Perry; Jeremy R Thompson
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

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