Literature DB >> 23438856

The "Observer Effect" in genome-wide surveys of protein-RNA interactions.

Kasandra J Riley1, Joan A Steitz.   

Abstract

Recent technological advances have spurred genome-wide studies that afford insights into ribonucleoprotein biology and transcript regulation on an unprecedented scale. Here we review techniques currently used to obtain genome-wide profiles of RNA-protein interactions in living cells. We highlight recent studies of the mRNA-bound proteome and address pitfalls inherent in such investigations.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID： 23438856      PMCID： PMC3719848          DOI： 10.1016/j.molcel.2013.01.030

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  28 in total

1.  A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1.

Authors:  Jane E Wright; Dimos Gaidatzis; Mathias Senften; Brian M Farley; Eric Westhof; Sean P Ryder; Rafal Ciosk
Journal:  EMBO J       Date:  2010-12-17       Impact factor: 11.598

2.  RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

Authors:  Jack D Keene; Jordan M Komisarow; Matthew B Friedersdorf
Journal:  Nat Protoc       Date:  2006       Impact factor: 13.491

3.  Association of Argonaute proteins and microRNAs can occur after cell lysis.

Authors:  Kasandra J Riley; Therese A Yario; Joan A Steitz
Journal:  RNA       Date:  2012-07-26       Impact factor: 4.942

4.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

Authors:  Ahmad M Khalil; Mitchell Guttman; Maite Huarte; Manuel Garber; Arjun Raj; Dianali Rivea Morales; Kelly Thomas; Aviva Presser; Bradley E Bernstein; Alexander van Oudenaarden; Aviv Regev; Eric S Lander; John L Rinn
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-01       Impact factor: 11.205

5.  CLIP identifies Nova-regulated RNA networks in the brain.

Authors:  Jernej Ule; Kirk B Jensen; Matteo Ruggiu; Aldo Mele; Aljaz Ule; Robert B Darnell
Journal:  Science       Date:  2003-11-14       Impact factor: 47.728

6.  Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.

Authors:  Aly A Khan; Doron Betel; Martin L Miller; Chris Sander; Christina S Leslie; Debora S Marks
Journal:  Nat Biotechnol       Date:  2009-06       Impact factor: 54.908

7.  PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Authors:  Markus Hafner; Markus Landthaler; Lukas Burger; Mohsen Khorshid; Jean Hausser; Philipp Berninger; Andrea Rothballer; Manuel Ascano; Anna-Carina Jungkamp; Mathias Munschauer; Alexander Ulrich; Greg S Wardle; Scott Dewell; Mihaela Zavolan; Thomas Tuschl
Journal:  J Vis Exp       Date:  2010-07-02       Impact factor: 1.355

8.  Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.

Authors:  Sung Wook Chi; Julie B Zang; Aldo Mele; Robert B Darnell
Journal:  Nature       Date:  2009-06-17       Impact factor: 49.962

Review 9.  RNA-binding proteins and post-transcriptional gene regulation.

Authors:  Tina Glisovic; Jennifer L Bachorik; Jeongsik Yong; Gideon Dreyfuss
Journal:  FEBS Lett       Date:  2008-03-13       Impact factor: 4.124

10.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

Authors:  Donny D Licatalosi; Aldo Mele; John J Fak; Jernej Ule; Melis Kayikci; Sung Wook Chi; Tyson A Clark; Anthony C Schweitzer; John E Blume; Xuning Wang; Jennifer C Darnell; Robert B Darnell
Journal:  Nature       Date:  2008-11-02       Impact factor: 49.962
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  40 in total

1.  Systematic discovery of Xist RNA binding proteins.

Authors:  Ci Chu; Qiangfeng Cliff Zhang; Simão Teixeira da Rocha; Ryan A Flynn; Maheetha Bharadwaj; J Mauro Calabrese; Terry Magnuson; Edith Heard; Howard Y Chang
Journal:  Cell       Date:  2015-04-02       Impact factor: 41.582

2.  Techniques for Characterizing Cytomegalovirus-Encoded miRNAs.

Authors:  Nicole L Diggins; Lindsey B Crawford; Hillary M Struthers; Lauren M Hook; Igor Landais; Rebecca L Skalsky; Meaghan H Hancock
Journal:  Methods Mol Biol       Date:  2021

3.  Imaging mRNA and protein interactions within neurons.

Authors:  Carolina Eliscovich; Shailesh M Shenoy; Robert H Singer
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

Review 4.  Probing RNA-protein networks: biochemistry meets genomics.

Authors:  Zachary T Campbell; Marvin Wickens
Journal:  Trends Biochem Sci       Date:  2015-01-27       Impact factor: 13.807

5.  Leveraging the complementary nature of RNA-Seq and shotgun proteomics data.

Authors:  Xiaojing Wang; Qi Liu; Bing Zhang
Journal:  Proteomics       Date:  2014-11-17       Impact factor: 3.984

6.  SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.

Authors:  Matthew J Smola; Thomas W Christy; Kaoru Inoue; Cindo O Nicholson; Matthew Friedersdorf; Jack D Keene; David M Lee; J Mauro Calabrese; Kevin M Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-30       Impact factor: 11.205

Review 7.  Bioinformatic tools for analysis of CLIP ribonucleoprotein data.

Authors:  Supriyo De; Myriam Gorospe
Journal:  Wiley Interdiscip Rev RNA       Date:  2016-12-23       Impact factor: 9.957

8.  Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis.

Authors:  Christopher P Lapointe; Jonathan A Stefely; Adam Jochem; Paul D Hutchins; Gary M Wilson; Nicholas W Kwiecien; Joshua J Coon; Marvin Wickens; David J Pagliarini
Journal:  Cell Syst       Date:  2017-12-13       Impact factor: 10.304

Review 9.  A brave new world of RNA-binding proteins.

Authors:  Matthias W Hentze; Alfredo Castello; Thomas Schwarzl; Thomas Preiss
Journal:  Nat Rev Mol Cell Biol       Date:  2018-01-17       Impact factor: 94.444

10.  Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins.

Authors:  Je-Hyun Yoon; Myriam Gorospe
Journal:  Methods Mol Biol       Date:  2016
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