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Literature DB >> 23334102

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.

Mohsen Khorshid¹, Jean Hausser, Mihaela Zavolan, Erik van Nimwegen.

Abstract

We introduce a biophysical model of miRNA-target interaction and infer its parameters from Argonaute 2 cross-linking and immunoprecipitation data. We show that a substantial fraction of human miRNA target sites are noncanonical and that predicted target-site affinity correlates well with the extent of target destabilization. Our model provides a rigorous biophysical approach to miRNA target identification beyond ad hoc miRNA seed-based methods.

Entities: Gene Species

Mesh：

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Year: 2013 PMID： 23334102 DOI： 10.1038/nmeth.2341

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

23 in total

1. MicroRNA targeting specificity in mammals: determinants beyond seed pairing.

Authors: Andrew Grimson; Kyle Kai-How Farh; Wendy K Johnston; Philip Garrett-Engele; Lee P Lim; David P Bartel
Journal: Mol Cell Date: 2007-07-06 Impact factor: 17.970

2. Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression.

Authors: Peter S Linsley; Janell Schelter; Julja Burchard; Miho Kibukawa; Melissa M Martin; Steven R Bartz; Jason M Johnson; Jordan M Cummins; Christopher K Raymond; Hongyue Dai; Nelson Chau; Michele Cleary; Aimee L Jackson; Michael Carleton; Lee Lim
Journal: Mol Cell Biol Date: 2007-01-22 Impact factor: 4.272

3. Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines.

Authors: S-K Leivonen; R Mäkelä; P Ostling; P Kohonen; S Haapa-Paananen; K Kleivi; E Enerly; A Aakula; K Hellström; N Sahlberg; V N Kristensen; A-L Børresen-Dale; P Saviranta; M Perälä; O Kallioniemi
Journal: Oncogene Date: 2009-08-17 Impact factor: 9.867

4. miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements.

Authors: Ashish Lal; Francisco Navarro; Christopher A Maher; Laura E Maliszewski; Nan Yan; Elizabeth O'Day; Dipanjan Chowdhury; Derek M Dykxhoorn; Perry Tsai; Oliver Hofmann; Kevin G Becker; Myriam Gorospe; Winston Hide; Judy Lieberman
Journal: Mol Cell Date: 2009-09-11 Impact factor: 17.970

5. An alternative mode of microRNA target recognition.

Authors: Sung Wook Chi; Gregory J Hannon; Robert B Darnell
Journal: Nat Struct Mol Biol Date: 2012-02-12 Impact factor: 15.369

6. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.

Authors: Jian-Hua Yang; Jun-Hao Li; Peng Shao; Hui Zhou; Yue-Qin Chen; Liang-Hu Qu
Journal: Nucleic Acids Res Date: 2010-10-30 Impact factor: 16.971

7. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.

Authors: David M Garcia; Daehyun Baek; Chanseok Shin; George W Bell; Andrew Grimson; David P Bartel
Journal: Nat Struct Mol Biol Date: 2011-09-11 Impact factor: 15.369

8. ViennaRNA Package 2.0.

Authors: Ronny Lorenz; Stephan H Bernhart; Christian Höner Zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal: Algorithms Mol Biol Date: 2011-11-24 Impact factor: 1.405

9. microRNA target predictions across seven Drosophila species and comparison to mammalian targets.

Authors: Dominic Grün; Yi-Lu Wang; David Langenberger; Kristin C Gunsalus; Nikolaus Rajewsky
Journal: PLoS Comput Biol Date: 2005-06-24 Impact factor: 4.475

10. Principles of microRNA-target recognition.

Authors: Julius Brennecke; Alexander Stark; Robert B Russell; Stephen M Cohen
Journal: PLoS Biol Date: 2005-03 Impact factor: 8.029

75 in total

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Authors: Xiaowei Wang
Journal: Bioinformatics Date: 2016-01-06 Impact factor: 6.937

2. Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.

Authors: Stefanie Grosswendt; Andrei Filipchyk; Mark Manzano; Filippos Klironomos; Marcel Schilling; Margareta Herzog; Eva Gottwein; Nikolaus Rajewsky
Journal: Mol Cell Date: 2014-05-22 Impact factor: 17.970

3. Menage a Trois: intimate relationship among a microRNA, long noncoding RNA, and mRNA.

Authors: Gerald W Dorn; Scot J Matkovich
Journal: Circ Res Date: 2014-04-25 Impact factor: 17.367

4. miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.

Authors: Jochen Imig; Andreas Brunschweiger; Anneke Brümmer; Boris Guennewig; Nitish Mittal; Shivendra Kishore; Panagiota Tsikrika; André P Gerber; Mihaela Zavolan; Jonathan Hall
Journal: Nat Chem Biol Date: 2014-12-22 Impact factor: 15.040

5. High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2.

Authors: Winston R Becker; Benjamin Ober-Reynolds; Karina Jouravleva; Samson M Jolly; Phillip D Zamore; William J Greenleaf
Journal: Mol Cell Date: 2019-07-16 Impact factor: 17.970

6. From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.

Authors: Silvia Bottini; Nedra Hamouda-Tekaya; Bogdan Tanasa; Laure-Emmanuelle Zaragosi; Valerie Grandjean; Emanuela Repetto; Michele Trabucchi
Journal: Nucleic Acids Res Date: 2017-05-19 Impact factor: 16.971