RNA–RNA interactions in gene regulation: the coding and noncoding players

• A variety of RNAs engage in direct RNA–RNA interactions with regulatory potential.
• These multiple interactions are interconnected and create complex cellular networks.
• RNA-based circuitries may underlie both physiological and disease-related cell states.

The past few years have witnessed an exciting increase in the richness and complexity of RNA-mediated regulatory circuitries, including new types of RNA–RNA interaction that underlie key steps in gene expression control in an organized and probably hierarchic system to dictate final protein output. Both small (especially miRNAs) and long coding (lc) and noncoding (nc) RNAs contain structural domains that can sense and bind other RNAs via complementary base pairing. The versatility of the interaction confers multiple roles to RNA–RNA hybrids, from control of RNA biogenesis to competition for common targets. Here, we focus on the emerging evidence around RNA networks and their impact on gene expression regulation in light of recent breakthroughs around the crosstalk between coding RNAs and ncRNAs.