mGem: Horses for courses in mapping bacterial small RNA interaction networks

Over the past few decades, it has become increasingly clear that small RNAs (sRNAs) play important regulatory roles in bacteria. These RNA species often work in concert with RNA chaperones such as Hfq that facilitate their base-pairing with target mRNAs. The mapping of sRNA interaction networks through the identification of the RNA species that sRNAs base-pair with can therefore provide critical insights into the potential regulatory roles sRNAs play. Indeed, sRNA interaction networks can be complex, with some bacteria producing more than a hundred different sRNAs, each capable of targeting anywhere from a single mRNA to several hundred different mRNAs. Here, we highlight two high-throughput approaches, RNA interaction by ligation and sequencing and intracellular RNA interaction by ligation and sequencing, that enable transcriptome-wide identification of sRNA interaction partners. Both methods capture RNA-RNA interactions in vivo and exploit chaperone-associated RNA-RNA ligation to capture native sRNA-target duplexes, providing powerful and scalable strategies for determining bacterial sRNA interaction networks.