A functional genomics screen for microRNA regulators of NF-kappaB signaling
Open Access
- 28 February 2013
- journal article
- Published by Springer Science and Business Media LLC in BMC Biology
- Vol. 11 (1), 19
- https://doi.org/10.1186/1741-7007-11-19
Abstract
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. 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. 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
This publication has 57 references indexed in Scilit:
- miR-301a as an NF-κB activator in pancreatic cancer cellsThe EMBO Journal, 2010
- STAT3 Activation of miR-21 and miR-181b-1 via PTEN and CYLD Are Part of the Epigenetic Switch Linking Inflammation to CancerMolecular Cell, 2010
- Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIPCell, 2010
- Frequent Amplification of a chr19q13.41 MicroRNA Polycistron in Aggressive Primitive Neuroectodermal Brain TumorsCancer Cell, 2009
- What have RNAi screens taught us about viral–host interactions?Current Opinion in Microbiology, 2009
- MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed PairingMolecular Cell, 2007
- MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in MammalsMolecular Cell, 2007
- Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR EvolutionCell, 2005
- Identification of hundreds of conserved and nonconserved human microRNAsNature Genetics, 2005
- Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA TargetsCell, 2005