Intronic miRNA mediated gene expression regulation controls protein crowding inside the cell.

Abstract Gene regulatory effects of microRNAs at a posttranscriptional level have been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, chemical kinetics, co-localization, concentration levels, network parameters and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration. Here we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily 'pause' the translation of mRNA, indicating that the miRNA–mRNA interactions may be important for governing the optimal usage of cell volume. Highlights • Genome scale analysis of spatio-temporal regulation of translation by intronic miRNA and its target genes. • Intronic miRNA mediated regulation is predominately in molecular transport, translational regulation and apoptotic processes. • The analysis points out that intronic miRNA mediated translational regulation could control protein crowding inside the cell. • Intronic miRNA mediated regulation is proposed to be a pause function in gene regulation for systematic expression of proteins. • The present study opens up the possibility to design experiments to control cellular transport and apoptosis. [ABSTRACT FROM AUTHOR]