Genome Mapping of RNA-DNA Hybrids in Escherichia coli

We have mapped RNA-DNA hybrids in the prokaryotic genome for the first time. Using the S9.6 antibody immunoprecipitation method (S9.6-DRIP) followed by whole-genome sequencing, we identified 219 unique peaks of RNA-DNA hybrids in the genome of Escherichia coli TOP10. These peaks corresponded to 219 different genes and were predominantly distributed in the coding regions of the genome (88.12%). Analysis of individual genes containing RNA-DNA hybrids revealed that they encode enzymes involved in important energy and metabolic processes in prokaryotes, such as lipoic acid synthesis.