MicroRNA networks alter to conform to transcription factor networks adding redundancy and reducing the repertoire of target genes for coordinated regulation

Abstract

Transcription factors (TFs) and microRNAs (miRNAs) comprise two major layers of gene regulatory networks (GRNs). TFs and miRNAs function coordinately, but they have distinct molecular mechanisms and evolutionary backgrounds. Therefore, we aimed to systematically reveal the difference in contribution between TF and miRNA networks to the evolution of their coordinated regulations by focusing on composite feedforward circuits (cFFCs) that each comprises a TF and an miRNA. We compiled 124,736 human-mouse conserved TF regulatory connections and 34,298 conserved miRNA regulatory connections into two distinct connection matrices. To differentially assess the contributions to cFFC formation of TFs and miRNAs, we randomized one matrix and kept the other unchanged and subsequently examined the number of cFFCs, the number of cFFC-targeted genes, and the redundancy formed by cFFCs in comparison with those of the real GRNs. Because the matrices represent selectively constrained networks, if selection has been operating on the networks for or against cFFC formation, the values of cFFC network properties would deviate significantly from the expectation of the randomized networks. As the cFFC includes both TF and miRNA connections, the partial randomizations indicate the extent of influence of selection on cFFC formation differentially between TF and miRNA networks. Thus, we adopted the deviation of each cFFC network property value as a measure to estimate the extent of influence of selection on cFFCs and to compare the contribution between TF and miRNA networks. We found that miRNA regulatory networks changed their configuration such that they conformed to the stable TF regulatory networks with an increased circuit redundancy and a marked reduction in the repertoire of cFFC-targeted genes. We also revealed that this redundancy-adding role is preferentially attributable to miRNA network alterations. The results indicate that the redundancy-adding role might serve as a niche for many miRNA connections to survive, avoiding conflicts with the stable TF regulatory networks.