Biological Insights from RNA–RNA Interactomes in Bacteria, as Revealed by RIL-seq

Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short RNA molecules that modulate gene expression usually through base-pairing interactions with target RNAs, primarily mRNAs. These interactions can lead to either negative outcomes such as mRNA degradation or translational repression or positive outcomes such as mRNA stabilization or translation enhancement. In recent years, high-throughput approaches such as RIL-seq (RNA interaction by ligation and sequencing) revolutionized the sRNA field by enabling the identification of sRNA targets on a global scale, unveiling intricate sRNA–RNA networks. In this review, we discuss the insights gained from investigating sRNA–RNA networks in well-studied bacterial species as well as in understudied bacterial species. Having a complete understanding of sRNA-mediated regulation is critical for the development of new strategies for controlling bacterial growth and combating bacterial infections.