Transcriptional Regulation of Gene Expression by microRNAs as Endogenous Decoys of Transcription Factors

Abstract

Background/Aims: MicroRNAs (miRNAs) are known to produce post-transcriptional repression of gene expression. In light of the ability of decoy oligodeocynucleotides (ODNs) to sequestrate transcription factors (TFs) and the similar double-stranded structure between decoy ODNs and miRNAs, we proposed that miRNAs might act as endogenous decoy molecules to produce transcriptional regulation of gene expression. Methods: Quantitative real-time RT-PCR analysis was used to measure the changes of miRNA and mRNA expression. Luciferase reporter gene activity assay was used to investigate the functional interaction between miRNAs and TFs. Electrophoresis mobility shift assay (EMSA) and modified chromatin immunoprecipitation assay (ChIP) were utilized to investigate the physical interactions between miRNAs and TFs. MTT cell viability assay and cellular DNA fragmentation ELISA were used to study apoptotic cell death. Results: We presented here that miRNAs could regulate, either negatively or positively, gene expression at the transcriptional level through its decoy-like actions and this mechanism operates under physiological conditions to produce cellular functions. We identified the putative cis-elements for transcriptional factors NF-κB and NFAT in the mature miR-939 and miR-376a, respectively. We experimentally established the ability of these miRNAs to physically bind their respective target TFs, using EMSA and ChIP methods. We then utilized the luciferase reporter gene assay to characterize the specific regulation of luciferase gene activities by miR-939/pre-miR-939:NF-κB or miR-376a/pre-miR-376a:NFAT interactions. Moreover, miR-939 and miR-376a produced transcriptional regulation of endogenous genes Bcl-xL and FasL/miR-26 that are the transcriptional targets for NF-kB and NFAT, respectively, but are not post-transcriptional targets for these two miRNAs. Finally, interference of these miRNAs with NF-κB and NFAT demonstrated clear phenotypes at the cellular level as manifested by the regulation of neuroblastoma cell death by miR-939 and miR-376a. Conclusion: Our study identified a novel non-canonical mechanism of miRNAs and suggests that when considering the cellular function of miRNAs the decoy-like mechanism for transcriptional regulation (activation or repression) should be taken into account.

Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939

“…A number of miRNAs have been implicated in the regulation of NFκB signaling 11 25 including miR-939. A noncanonical mechanism of action for miR-939 and NFκB was shown in a recent study 26 . miR-939 physically interacted with NFκB and this was mediated by the cis-elements present within the sequences of miR-939 for the p50 subunit of NFκB.…”

“…miR-939 physically interacted with NFκB and this was mediated by the cis-elements present within the sequences of miR-939 for the p50 subunit of NFκB. It was proposed that miR-939 can act as endogenous decoy molecules for NFκB 26 . Our in vitro studies and pathway analysis indicate that the regulation of NFκB expression by miR-939 can directly and indirectly impact several proinflammatory mediators.…”

Nuclear microRNAs in normal hemopoiesis and cancer

“…They include increased or decreased levels of histone modifications associated with gene activation [39, 45, 61], altered RNA Polymerase II activity [38, 61], enhanced recruitment of transcription factors [59] and inhibition of transcription factor binding due to the presence of decoy miRNAs [62]. …”

Identification and characterization of microRNAs and their target genes from Nile tilapia (Oreochromis niloticus)

“…The largest group contains 17 targets predicted to encode transcription factors. Transcription factor mRNAs are well-known targets of miRNAs in almost all plant and animal species [32]. The other 39 miRNA targets encode several functional groups of proteins involved in animal metabolisms, development, signal transduction and stress response.…”