MicroRNA Target Identification

2019 ◽  
Keyword(s):  
Target Identification ◽  
Microrna Target

Human microRNA target identification by RRSM

2011 ◽  
Vol 286 ◽  
pp. 79-84 ◽  
Author(s):  
Wan J. Hsieh ◽  
Hsiuying Wang
Keyword(s):  
Target Identification ◽  
Microrna Target

scholarly journals MicroRNA Target Identification—Experimental Approaches

Biology ◽  
2013 ◽  
Vol 2 (1) ◽  
pp. 189-205 ◽  
Author(s):  
Aida Martinez-Sanchez ◽  
Chris Murphy
Keyword(s):  
Target Identification ◽  
Microrna Target ◽  
Experimental Approaches

scholarly journals Experimental strategies for microRNA target identification

2011 ◽  
Vol 39 (16) ◽  
pp. 6845-6853 ◽  
Author(s):  
D. W. Thomson ◽  
C. P. Bracken ◽  
G. J. Goodall
Keyword(s):  
Target Identification ◽  
Microrna Target ◽  
Experimental Strategies

scholarly journals Contemporary Ribonomics Methods for Viral microRNA Target Analysis

2018 ◽  
Vol 4 (4) ◽  
pp. 31 ◽  
Author(s):  
Lauren Gay ◽  
Peter Turner ◽  
Rolf Renne
Keyword(s):  
High Throughput Sequencing ◽  
Rna Binding ◽  
Cultured Cells ◽  
Target Identification ◽  
Microrna Target ◽  
Link Protein ◽  
Barr Virus ◽  
Cellular Processes ◽  
Viral Microrna ◽  
Epstein Barr

Numerous cellular processes are regulated by microRNAs (miRNAs), both cellular and viral. Elucidating the targets of miRNAs has become an active area of research. An important method in this field is cross-linking and immunoprecipitation (CLIP), where cultured cells or tissues are UV-irradiated to cross-link protein and nucleic acid, the RNA binding protein of interest is immunoprecipitated, and the RNAs pulled down with the protein are isolated, reverse-transcribed, and analyzed by sequencing. CLIP using antibody against Argonaute (Ago), which binds to both miRNA and mRNA as they interact in RISC, has allowed researchers to uncover a large number of miRNA targets. Coupled with high-throughput sequencing, CLIP has been useful for revealing miRNA targetomes for the γ-herpesviruses Kaposi’s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). Variants on the CLIP protocol are described, with the benefits and drawbacks of each. In particular, the most recent methods involving RNA–RNA ligation to join the miRNA and its RNA target have aided in target identification. Lastly, data supporting biologically meaningful interactions between miRNAs and long non-coding RNAs (lncRNAs) are reviewed. In summary, ribonomics-based miRNA targetome analysis has expanded our understanding of miRNA targeting and has provided a rich resource for EBV and KSHV research with respect to pathogenesis and tumorigenesis.

MicroRNA Target Identification: Lessons from HypoxamiRs

2014 ◽  
Vol 21 (8) ◽  
pp. 1249-1268 ◽  
Author(s):  
Thomas Bertero ◽  
Karine Robbe-Sermesant ◽  
Kevin Le Brigand ◽  
Gilles Ponzio ◽  
Nicolas Pottier ◽  
...  
Keyword(s):  
Target Identification ◽  
Microrna Target

scholarly journals Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

2009 ◽  
Vol 5 (9) ◽  
pp. e1000516 ◽  
Author(s):  
Stephen A. Stanhope ◽  
Srikumar Sengupta ◽  
Johan den Boon ◽  
Paul Ahlquist ◽  
Michael A. Newton
Keyword(s):  
Target Identification ◽  
Microrna Target

scholarly journals Macros in microRNA target identification

RNA Biology ◽  
2014 ◽  
Vol 11 (4) ◽  
pp. 324-333 ◽  
Author(s):  
Shikha Tarang ◽  
Michael D Weston
Keyword(s):  
Target Identification ◽  
Microrna Target

What’s the target: understanding two decades of in silico microRNA-target prediction

2019 ◽  
Vol 21 (6) ◽  
pp. 1999-2010 ◽  
Author(s):  
Fabian Kern ◽  
Christina Backes ◽  
Pascal Hirsch ◽  
Tobias Fehlmann ◽  
Martin Hart ◽  
...  
Keyword(s):  
In Silico ◽  
Homo Sapiens ◽  
Target Identification ◽  
Target Prediction ◽  
Microrna Target ◽  
Transcriptional Regulatory ◽  
Recent Developments ◽  
Mature Micrornas ◽  
Initial Discovery ◽  
Set Up

Abstract Motivation Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of $2656$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up. Results In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools. Availability An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.

scholarly journals CRISPR screening strategies for microRNA target identification

FEBS Journal ◽  
2020 ◽  
Vol 287 (14) ◽  
pp. 2914-2922 ◽  
Author(s):  
Bing Yang ◽  
Katherine McJunkin
Keyword(s):  
Target Identification ◽  
Microrna Target ◽  
Screening Strategies
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