Journal
NUCLEIC ACIDS RESEARCH
Volume 47, Issue 20, Pages 10894-10905Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkz791
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Funding
- Doctoral program RNA Biology [W1207-B09]
- Austrian Science Fund (Fonds zur Forderung der wissenschaftlichen Forschung) [I538-B12, F4301, F4308]
- National Institutes of Health [R01 GM126891]
- Austrian Science Fund
- Blavatnik Family Foundation
- Howard Hughes Medical Institute
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RNA polymerase-binding RNA aptamers (RAPs) are natural RNA elements that control transcription in cis by directly contacting RNA polymerase. Many RAPs inhibit transcription by inducing Rho-dependent termination in Escherichia coli. Here, we studied the role of inhibitory RAPs (iRAPs) in modulation of antisense transcription (AT) using in silico and in vivo approaches. We revisited the antisense transcriptome in cells with impaired AT regulators (Rho, H-NS and RNaseIII) and searched for the presence of RAPs within antisense RNAs. Many of these RAPs were found at key genomic positions where they terminate AT. By exploring the activity of several RAPs both in a reporter system and in their natural genomic context, we confirmed their significant role in AT regulation. RAPs coordinate Rho activity at the antisense strand and terminate antisense transcripts. In some cases, they stimulated sense expression by alleviating ongoing transcriptional interference. Essentially, our data postulate RAPs as key determinants of Rho-mediated AT regulation in E. coli.
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