Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network

Abstract

MicroRNAs (miRs) are small RNAs that regulate gene expression at the posttranscriptional level. It is anticipated that, in combination with transcription factors (TFs), they span a regulatory network that controls thousands of mammalian genes. Here we set out to uncover local and global architectural features of the mammalian miR regulatory network. Using evolutionarily conserved potential binding sites of miRs in human targets, and conserved binding sites of TFs in promoters, we uncovered two regulation networks. The first depicts combinatorial interactions between pairs of miRs with many shared targets. The network reveals several levels of hierarchy, whereby a few miRs interact with many other lowly connected miR partners. We revealed hundreds of “target hubs” genes, each potentially subject to massive regulation by dozens of miRs. Interestingly, many of these target hub genes are transcription regulators and they are often related to various developmental processes. The second network consists of miR–TF pairs that coregulate large sets of common targets. We discovered that the network consists of several recurring motifs. Most notably, in a significant fraction of the miR–TF coregulators the TF appears to regulate the miR, or to be regulated by the miR, forming a diversity of feed-forward loops. Together these findings provide new insights on the architecture of the combined transcriptional–post transcriptional regulatory network. It is becoming increasingly appreciated that a new type of gene which does not code for proteins, the regulatory RNAs, constitutes a considerable portion of mammalian genomes, and these genes serve as key players in the regulatory network of living cells. Among these regulatory RNAs are the microRNAs (miRs), small RNAs that mediate posttranscriptional gene silencing through inhibition of protein production or degradation of mRNAs. So far little is known about the extent of regulation by miRs, and their potential cooperation with other regulatory layers in the network. We investigated the potential crosstalk between the miR-mediated posttranscription layer, and the transcriptional regulation layer, whose dominant players, the transcription factors (TFs), regulate the production of protein-coding mRNAs. We found that the extent of miR regulation varies extensively among different genes, some of which, especially those who serve as regulators themselves, are subject to enhanced miR silencing. Further, we identified thousands of genes that are potentially subjected to coordinated regulation by multiple miRs and by specific combinations of TFs and miRs. The regulatory network, comprising transcriptional and posttranscriptional regulation, manifests several recurring architectures, one of which consists of a TF and a miR that together regulate a large set of common genes, and that also appear to regulate one another. Altogether this work provides new insights into the logic and evolution of a new regulatory layer of the mammalian genome, and its effect on other regulatory networks in the cell.