Emerging roles of RNA modifications in bacteria

RNA modifications are known to abound in stable tRNA and rRNA, where they cluster around functionally important regions. However, RNA-seq based techniques profiling entire transcriptomes are now uncovering an abundance of modified ribonucleotides in mRNAs and noncoding RNAs, too. While most of the recent progress in understanding the regulatory influence of these new RNA modifications stems from eukaryotes, there is growing evidence in bacteria for modified nucleotides beyond the stable RNA species, including modifications of small regulatory RNAs. Given their small genome size, good genetic tractability, and ample knowledge of modification enzymes, bacteria offer excellent model systems to decipher cellular functions of RNA modifications in many diverse physiological contexts. This review highlights how new global approaches combining classic analysis with new sequencing techniques may usher in an era of bacterial epitranscriptomics.