MicroRNAs coordinately regulate protein complexes

Abstract

Background: In animals, microRNAs (miRNAs) regulate the protein synthesis of their target messenger RNAs (mRNAs) by either translational repression or deadenylation. miRNAs are frequently found to be co-expressed in different tissues and cell types, while some form polycistronic clusters on genomes. Interactions between targets of co-expressed miRNAs (including miRNA clusters) have not yet been systematically investigated.

Results: Here we integrated information from predicted and experimentally verified miRNA targets to characterize protein complex networks regulated by human miRNAs. We found striking evidence that individual miRNAs or co-expressed miRNAs frequently target several components of protein complexes. We experimentally verified that the miR-141-200c cluster targets different components of the CtBP/ZEB complex, suggesting a potential orchestrated regulation in epithelial to mesenchymal transition.

Conclusions: Our findings indicate a coordinate posttranscriptional regulation of protein complexes by miRNAs. These provide a sound basis for designing experiments to study miRNA function at a systems level.

Figure 1

Functional analysis and validation of miRNA-regulated protein complexes. Functional analysis: Enrichment of Gene Ontology (GO) terms and KEGG pathways in the target subunits of protein complexes. The size of the bars for each term indicates the negative logarithm of the P-value. Only meaningful and non-redundant terms were selected for illustration. See Additional file 3 &4, Table S3&S4 for a complete and detailed list of significant terms.

Figure 2

Validation of targeted complex components. Fold change distributions of targeted and non-targeted proteins in complexes for each investigated miRNA. The (*) indicates high significance in the Kolmogorov-Smirnov test.

Figure 3

Statistical evidence of coordinate regulation by miRNAs. a, Pearson correlation distributions of miRNAs that target the same complex (red line) is plotted against the distribution of all observed Pearson correlation values (black dotted line). Also the distributions of excluded Pearson correlations of miRNAs from the same family (blue) and the same cluster (green) are plotted. b, Boxplot for direct interactions of proteins targeted by N miRNAs within a cluster as compared to a null model of N randomly sampled miRNAs, respectively.

Figure 4

Protein complexes regulated by the miR-141-200c cluster. a, Real-time reverse transcription-PCR of CtBP2 and ZEB1 after transfection of the indicated miRNAs in undifferentiated cancer cells (PANC-1). The expression levels of E-cadherin (of which the transcription is repressed by CtBP/ZEB complex) are included as positive controls. b, Confirmation of the regulation of CtBP2 and ZEB1 by miR-141 and miR-200c on protein levels by immunoblots. c, ZEB1 and CtBP2 knock down by siRNAs, no change in protein levels of the respective complex partner is oberserved. e, Downregulation of CDYL and RCOR3 on protein level when miR-141 or miR-200c was transiently transfected.