DNA–RNA interactions are critical for chromosome condensation in Escherichia coli

Significance This study focuses on the molecular mechanisms of a noncoding RNA-mediated chromosome organization in Escherichia coli . We show for the first time that noncoding RNA, naRNA4, a critical element at least in part of chromosome structural organization (DNA condensation), may form DNA–RNA complexes in an uncommon way. Surprisingly, we found that HU protein catalyzes the DNA–RNA interactions without being part of the “final” complexes. There are several important examples of noncoding RNA playing critical roles in eukaryotic chromatin functioning, e.g., heterochromatin assembly, gene silencing, and X-inactivation, although nothing is known about the nature of DNA–RNA interaction(s) in these processes. Our findings will be of great interest in the chromatin field, providing mechanistic insights into the large-scale organization of DNA.