Document Detail


An arrayed RNA interference genome-wide screen identifies candidate genes involved in the MicroRNA 21 biogenesis pathway.
MedLine Citation:
PMID:  23153064     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MicroRNAs (miRNAs) are evolutionary conserved noncoding molecules that regulate gene expression. They influence a number of diverse biological functions, such as development and differentiation. However, their dysregulation has been shown to be associated with disease states, such as cancer. Genes and pathways regulating their biogenesis remain unknown and are highly sought after. For this purpose, we have validated a multiplexed high-content assay strategy to screen for such modulators. Here, we describe its implementation that makes use of a cell-based gain-of-function reporter assay monitoring enhanced green fluorescent protein expression under the control of miRNA 21 (miR-21); combined with measures of both cell metabolic activities through the use of Alamar Blue and cell death through imaged Hoechst-stained nuclei. The strategy was validated using a panel of known genes and enabled us to successfully progress to and complete an arrayed genome-wide short interfering RNA (siRNA) screen against the Ambion Silencer Select v4.0 library containing 64,755 siRNA duplexes covering 21,565 genes. We applied a high-stringency hit analysis method, referred to as the Bhinder-Djaballah analysis method, leading to the nomination of 1,273 genes as candidate inhibitors of the miR-21 biogenesis pathway; after several iterations eliminating those genes with only one active duplex and those enriched in seed sequence mediated off-target effects. Biological classifications revealed four major control junctions among them vesicular transport via clathrin-mediated endocytosis. Altogether, our screen has uncovered a number of novel candidate regulators that are potentially good druggable targets allowing for the discovery and development of small molecules for regulating miRNA function.
Authors:
David Shum; Bhavneet Bhinder; Christina N Ramirez; Constantin Radu; Paul A Calder; Lesslie Beauchamp; T Farazi; M Landthaler; T Tuschi; Susan Magdaleno; Hakim Djaballah
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-11-15
Journal Detail:
Title:  Assay and drug development technologies     Volume:  11     ISSN:  1557-8127     ISO Abbreviation:  Assay Drug Dev Technol     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-04-08     Completed Date:  2013-09-25     Revised Date:  2014-04-09    
Medline Journal Info:
Nlm Unique ID:  101151468     Medline TA:  Assay Drug Dev Technol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  191-205     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Automation
Cells, Cultured
Coloring Agents
Gene Library
Gene Targeting
Green Fluorescent Proteins
High-Throughput Screening Assays
Humans
Image Processing, Computer-Assisted
MicroRNAs / biosynthesis*,  drug effects,  genetics*
Oxazines
Polymerase Chain Reaction
RNA Interference*
RNA, Small Interfering / genetics
Reproducibility of Results
Xanthenes
Grant Support
ID/Acronym/Agency:
5 P30 CA008748-44/CA/NCI NIH HHS; P30 CA008748/CA/NCI NIH HHS
Chemical
Reg. No./Substance:
0/Coloring Agents; 0/MIRN21 microRNA, human; 0/MicroRNAs; 0/Oxazines; 0/RNA, Small Interfering; 0/Xanthenes; 147336-22-9/Green Fluorescent Proteins; 550-82-3/resazurin
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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