Literature DB >> 29967010

Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome.

Chun Kit Kwok1, Giovanni Marsico2,3, Shankar Balasubramanian2,3.   

Abstract

RNA G-quadruplex (rG4) secondary structures are proposed to play key roles in fundamental biological processes that include the modulation of transcriptional, co-transcriptional, and posttranscriptional events. Recent methodological developments that include predictive algorithms and structure-based sequencing have enabled the detection and mapping of rG4 structures on a transcriptome-wide scale at high sensitivity and resolution. The data generated by these studies provide valuable insights into the potentially diverse roles of rG4s in biology and open up a number of mechanistic hypotheses. Herein we highlight these methodologies and discuss the associated findings in relation to rG4-related biological mechanisms.
Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2018        PMID: 29967010      PMCID: PMC6028067          DOI: 10.1101/cshperspect.a032284

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  82 in total

1.  Use of dimethyl sulfate to probe RNA structure in vivo.

Authors:  S E Wells; J M Hughes; A H Igel; M Ares
Journal:  Methods Enzymol       Date:  2000       Impact factor: 1.600

2.  In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei.

Authors:  C Schaffitzel; I Berger; J Postberg; J Hanes; H J Lipps; A Plückthun
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-03       Impact factor: 11.205

3.  Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments.

Authors:  Alina Selega; Christel Sirocchi; Ira Iosub; Sander Granneman; Guido Sanguinetti
Journal:  Nat Methods       Date:  2016-11-07       Impact factor: 28.547

4.  Suppression of gene expression by G-quadruplexes in open reading frames depends on G-quadruplex stability.

Authors:  Tamaki Endoh; Yu Kawasaki; Naoki Sugimoto
Journal:  Angew Chem Int Ed Engl       Date:  2013-04-15       Impact factor: 15.336

5.  Determination of in vivo RNA structure in low-abundance transcripts.

Authors:  Chun Kit Kwok; Yiliang Ding; Yin Tang; Sarah M Assmann; Philip C Bevilacqua
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

6.  Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines.

Authors:  Xueyin Wang; Karen J Goodrich; Anne R Gooding; Haroon Naeem; Stuart Archer; Richard D Paucek; Daniel T Youmans; Thomas R Cech; Chen Davidovich
Journal:  Mol Cell       Date:  2017-03-16       Impact factor: 17.970

Review 7.  5'-UTR RNA G-quadruplexes: translation regulation and targeting.

Authors:  Anthony Bugaut; Shankar Balasubramanian
Journal:  Nucleic Acids Res       Date:  2012-02-20       Impact factor: 16.971

8.  Gene function correlates with potential for G4 DNA formation in the human genome.

Authors:  Johanna Eddy; Nancy Maizels
Journal:  Nucleic Acids Res       Date:  2006-08-10       Impact factor: 16.971

9.  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

10.  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

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  32 in total

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2.  Diabetes enhances translation of Cd40 mRNA in murine retinal Müller glia via a 4E-BP1/2-dependent mechanism.

Authors:  Sadie K Dierschke; Allyson L Toro; William P Miller; Siddharth Sunilkumar; Michael D Dennis
Journal:  J Biol Chem       Date:  2020-05-31       Impact factor: 5.157

3.  Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA.

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4.  Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data.

Authors:  Matteo Castelli; Filippo Doria; Mauro Freccero; Giorgio Colombo; Elisabetta Moroni
Journal:  J Chem Theory Comput       Date:  2022-06-06       Impact factor: 6.578

Review 5.  Action and function of helicases on RNA G-quadruplexes.

Authors:  Marco Caterino; Katrin Paeschke
Journal:  Methods       Date:  2021-09-10       Impact factor: 4.647

6.  RNA G-quadruplex structure contributes to cold adaptation in plants.

Authors:  Xiaofei Yang; Haopeng Yu; Susan Duncan; Yueying Zhang; Jitender Cheema; Haifeng Liu; J Benjamin Miller; Jie Zhang; Chun Kit Kwok; Huakun Zhang; Yiliang Ding
Journal:  Nat Commun       Date:  2022-10-20       Impact factor: 17.694

Review 7.  Biogenesis and Functions of Circular RNAs Come into Focus.

Authors:  Mei-Sheng Xiao; Yuxi Ai; Jeremy E Wilusz
Journal:  Trends Cell Biol       Date:  2020-01-20       Impact factor: 20.808

8.  A guide to computational methods for G-quadruplex prediction.

Authors:  Emilia Puig Lombardi; Arturo Londoño-Vallejo
Journal:  Nucleic Acids Res       Date:  2020-01-10       Impact factor: 16.971

Review 9.  The regulation and functions of DNA and RNA G-quadruplexes.

Authors:  Dhaval Varshney; Jochen Spiegel; Katherine Zyner; David Tannahill; Shankar Balasubramanian
Journal:  Nat Rev Mol Cell Biol       Date:  2020-04-20       Impact factor: 94.444

10.  Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules.

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Journal:  Cancer Res       Date:  2021-02-25       Impact factor: 13.312

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