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Open Access Research article

A functional genomics screen for microRNA regulators of NF-kappaB signaling

Anthony O Olarerin-George13, Lauren Anton2, Yih-Chii Hwang1, Michal A Elovitz2 and John B Hogenesch13*

Author Affiliations

1 Genomics and Computational Biology Graduate Group, 1420 Blockley Hall, 423 Guardian Drive, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA

2 Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, 1354 Biomedical Research Building II/III, 421 Curie Blvd., Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA

3 Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, Smilow Translational Research Center 10-124, 3400 Civic Center Blvd., Bldg. 421, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA

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BMC Biology 2013, 11:19  doi:10.1186/1741-7007-11-19

Published: 28 February 2013

Abstract

Background

The nuclear factor-KappaB (NF-κB) pathway is conserved from fruit flies to humans and is a key mediator of inflammatory signaling. Aberrant regulation of NF-κB is associated with several disorders including autoimmune disease, chronic inflammation, and cancer, making the NF-κB pathway an attractive therapeutic target. Many regulatory components of the NF-κB pathway have been identified, including microRNAs (miRNAs). miRNAs are small non-coding RNAs and are common components of signal transduction pathways. Here we present a cell-based functional genomics screen to systematically identify miRNAs that regulate NF-κB signaling.

Results

We screened a library of miRNA mimics using a NF-κB reporter cell line in the presence and absence of tumor necrosis factor (+/- TNF). There were 9 and 15 hits in the -TNF and +TNF screens, respectively. We identified putative functional targets of these hits by integrating computational predictions with NF-κB modulators identified in a previous genome-wide cDNA screen. miR-517a and miR-517c were the top hits, activating the reporter 86- and 126-fold, respectively. Consistent with these results, miR-517a/c induced the expression of endogenous NF-κB targets and promoted the nuclear localization of p65 and the degradation of IκB. We identified TNFAIP3 interacting protein1 (TNIP1) as a target and characterized a functional SNP in the miR-517a/c binding site. Lastly, miR-517a/c induced apoptosis in vitro, which was phenocopied by knockdown of TNIP1.

Conclusions

Our study suggests that miRNAs are common components of NF-κB signaling and miR-517a/c may play an important role in linking NF-κB signaling with cell survival through TNIP1.

Keywords:
microRNA; miRNA; miR-517; NF-kappaB; TNIP1; TNF; RNAi; screen; apoptosis