Literature DB >> 27111506

irCLIP platform for efficient characterization of protein-RNA interactions.

Brian J Zarnegar1, Ryan A Flynn1,2, Ying Shen1, Brian T Do1,2, Howard Y Chang1,2, Paul A Khavari1,3.   

Abstract

The complexity of transcriptome-wide protein-RNA interaction networks is incompletely understood. While emerging studies are greatly expanding the known universe of RNA-binding proteins, methods for the discovery and characterization of protein-RNA interactions remain resource intensive and technically challenging. Here we introduce a UV-C crosslinking and immunoprecipitation platform, irCLIP, which provides an ultraefficient, fast, and nonisotopic method for the detection of protein-RNA interactions using far less material than standard protocols.

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Year:  2016        PMID： 27111506      PMCID： PMC5477425          DOI： 10.1038/nmeth.3840

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  20 in total

1.  A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles.

Authors:  Henning Urlaub; Klaus Hartmuth; Reinhard Lührmann
Journal:  Methods       Date:  2002-02       Impact factor: 3.608

2.  Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

Authors:  Svetlana Lebedeva; Marvin Jens; Kathrin Theil; Björn Schwanhäusser; Matthias Selbach; Markus Landthaler; Nikolaus Rajewsky
Journal:  Mol Cell       Date:  2011-06-30       Impact factor: 17.970

3.  Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells.

Authors:  Nils A Kulak; Garwin Pichler; Igor Paron; Nagarjuna Nagaraj; Matthias Mann
Journal:  Nat Methods       Date:  2014-02-02       Impact factor: 28.547

4.  Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.

Authors:  Alfredo Castello; Bernd Fischer; Katrin Eichelbaum; Rastislav Horos; Benedikt M Beckmann; Claudia Strein; Norman E Davey; David T Humphreys; Thomas Preiss; Lars M Steinmetz; Jeroen Krijgsveld; Matthias W Hentze
Journal:  Cell       Date:  2012-05-31       Impact factor: 41.582

5.  HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Authors:  Sebastien M Weyn-Vanhentenryck; Aldo Mele; Qinghong Yan; Shuying Sun; Natalie Farny; Zuo Zhang; Chenghai Xue; Margaret Herre; Pamela A Silver; Michael Q Zhang; Adrian R Krainer; Robert B Darnell; Chaolin Zhang
Journal:  Cell Rep       Date:  2014-03-06       Impact factor: 9.423

6.  Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing.

Authors:  Sabine Mohr; Eman Ghanem; Whitney Smith; Dennis Sheeter; Yidan Qin; Olga King; Damon Polioudakis; Vishwanath R Iyer; Scott Hunicke-Smith; Sajani Swamy; Scott Kuersten; Alan M Lambowitz
Journal:  RNA       Date:  2013-05-22       Impact factor: 4.942

7.  Dissecting noncoding and pathogen RNA-protein interactomes.

Authors:  Ryan A Flynn; Lance Martin; Robert C Spitale; Brian T Do; Selena M Sagan; Brian Zarnegar; Kun Qu; Paul A Khavari; Stephen R Quake; Peter Sarnow; Howard Y Chang
Journal:  RNA       Date:  2014-11-19       Impact factor: 4.942

8.  Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.

Authors:  Kathi Zarnack; Julian König; Mojca Tajnik; Iñigo Martincorena; Sebastian Eustermann; Isabelle Stévant; Alejandro Reyes; Simon Anders; Nicholas M Luscombe; Jernej Ule
Journal:  Cell       Date:  2013-01-31       Impact factor: 41.582

9.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

Authors:  Julian König; Kathi Zarnack; Gregor Rot; Tomaz Curk; Melis Kayikci; Blaz Zupan; Daniel J Turner; Nicholas M Luscombe; Jernej Ule
Journal:  Nat Struct Mol Biol       Date:  2010-07-04       Impact factor: 15.369

10.  iCLIP: protein-RNA interactions at nucleotide resolution.

Authors:  Ina Huppertz; Jan Attig; Andrea D'Ambrogio; Laura E Easton; Christopher R Sibley; Yoichiro Sugimoto; Mojca Tajnik; Julian König; Jernej Ule
Journal:  Methods       Date:  2013-10-25       Impact factor: 3.608
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  95 in total

Review 1.  Approaches for measuring the dynamics of RNA-protein interactions.

Authors:  Donny D Licatalosi; Xuan Ye; Eckhard Jankowsky
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-08-20       Impact factor: 9.957

2.  RNA-protein interaction detection in living cells.

Authors:  Muthukumar Ramanathan; Karim Majzoub; Deepti S Rao; Poornima H Neela; Brian J Zarnegar; Smarajit Mondal; Julien G Roth; Hui Gai; Joanna R Kovalski; Zurab Siprashvili; Theo D Palmer; Jan E Carette; Paul A Khavari
Journal:  Nat Methods       Date:  2018-02-05       Impact factor: 28.547

3.  SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein-RNA interactions with high accuracy.

Authors:  Ya Zhao; Yao Zhang; Yilan Teng; Kai Liu; Yanqing Liu; Weihua Li; Ligang Wu
Journal:  Nucleic Acids Res       Date:  2019-04-08       Impact factor: 16.971

Review 4.  Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools.

Authors:  Marlene Belfort; Alan M Lambowitz
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-04-01       Impact factor: 10.005

5.  The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.

Authors:  Lilli Olgeiser; Carl Haag; Susan Boerner; Jernej Ule; Anke Busch; Janine Koepke; Julian König; Michael Feldbrügge; Kathi Zarnack
Journal:  EMBO Rep       Date:  2018-12-14       Impact factor: 8.807

6.  A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.

Authors:  Dimitrios G Anastasakis; Alexis Jacob; Parthena Konstantinidou; Kazuyuki Meguro; Duncan Claypool; Pavol Cekan; Astrid D Haase; Markus Hafner
Journal:  Nucleic Acids Res       Date:  2021-05-07       Impact factor: 16.971

7.  TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.

Authors:  Yan Xu; Yan Chen; Daliang Li; Qing Liu; Zhenyu Xuan; Wen-Hong Li
Journal:  RNA Biol       Date:  2016-12-16       Impact factor: 4.652

8.  Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.

Authors:  Zhenrui Li; Pengxu Qian; Wanqing Shao; Hailing Shi; Xi C He; Madelaine Gogol; Zulin Yu; Yongfu Wang; Meijie Qi; Yunfei Zhu; John M Perry; Kai Zhang; Fang Tao; Kun Zhou; Deqing Hu; Yingli Han; Chongbei Zhao; Richard Alexander; Hanzhang Xu; Shiyuan Chen; Allison Peak; Kathyrn Hall; Michael Peterson; Anoja Perera; Jeffrey S Haug; Tari Parmely; Hua Li; Bin Shen; Julia Zeitlinger; Chuan He; Linheng Li
Journal:  Cell Res       Date:  2018-07-31       Impact factor: 25.617

Review 9.  The Future of Cross-Linking and Immunoprecipitation (CLIP).

Authors:  Jernej Ule; Hun-Way Hwang; Robert B Darnell
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-08-01       Impact factor: 10.005

10.  Easier, Better, Faster, Stronger: Improved Methods for RNA-Protein Interaction Studies.

Authors:  Nazmul Haque; J Robert Hogg
Journal:  Mol Cell       Date:  2016-06-02       Impact factor: 17.970
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