RAPs in control of antisense transcription in E. coli

RNA polymerase-binding RNA aptamers (RAPs) are natural RNA elements that control transcription in cis via direct contact with RNA polymerase (RNAP). Many of these aptamers inhibit transcription by causing Rho-dependent termination in Escherichia coli. Using in silico and in vivo approaches, here we studied the role of RAPs in modulation of antisense transcription (AT). We revisited the antisense transcriptome in cells with impaired major AT regulators (Rho, H-NS and RNaseIII) and searched for the presence of RAPs within antisense RNAs. A striking number of these aptamers were found in key positions to terminate AT. By exploring the activity of several RAPs in both reporter system and their natural genomic context, we could further confirm them playing a significant role in AT regulation. RAPs coordinate the Rho activity at the antisense strand and terminate antisense transcripts, in some cases additionally stimulating sense expression via alleviating ongoing transcriptional interference (TI). Essentially, our data postulate RAPs as key determinants of Rho-mediated regulation of AT in E. coli.