Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network

Abstract

Transcriptional regulation of gene expression is an essential cellular process that is arranged by transcription factors (TFs), microRNAs (miRNA) and their target genes through a variety of mechanisms. Here, we set out to reconstruct a comprehensive transcriptional regulatory network of Homo sapiens consisting of experimentally verified regulatory information on miRNAs, TFs and their target genes. We have performed topological analyses to elucidate the transcriptional regulatory roles of miRNAs and TFs. When we thoroughly investigated the network motifs, different gene regulatory scenarios were observed; whereas, mutual TF-miRNA regulation (interactive cooperation) and hierarchical operation where miRNAs were the upstream regulators of TFs came into prominence. Otherwise, biological process specific subnetworks were also constructed and integration of gene and miRNA expression data on ovarian cancer was achieved as a case study to observe dynamic patterns of the gene expression. Meanwhile, both co-operation and hierarchical operation types were determined in active ovarian cancer and process-specific subnetworks. In addition, the analysis showed that multiple signals from miRNAs were integrated by TFs. Our results demonstrate new insights on the architecture of the human transcriptional regulatory network, and here we present some lessons we gained from deciphering the reciprocal interplay between miRNAs, TFs and their target genes.