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| Status |
Public on Jun 01, 2017 |
| Title |
Natural RNA polymerase aptamers regulate transcription in E. coli [SELEX] |
| Organism |
Escherichia coli |
| Experiment type |
Other
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| Summary |
In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing growth conditions. The mechanism of iRAPs involves active uncoupling of transcription and translation, making the nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.
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| Overall design |
Examination of RNAP-binding aptamers in E. coli based on a single paired-end SELEX library sequenced on an Illumina GA Iix
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| Contributor(s) |
Sedlyarova N, Rescheneder P, Magán García A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E |
| Citation(s) |
28648779 |
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| Submission date |
May 08, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Philipp Rescheneder |
| E-mail(s) |
philipp.rescheneder@univie.ac.at
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| Organization name |
MFPL
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| Street address |
Dr. Bohr Gasse 9
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (1) |
| GPL18945 |
Illumina Genome Analyzer IIx (Escherichia coli) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE98661 |
Natural RNA polymerase aptamers regulate transcription in E. coli |
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| Relations |
| BioProject |
PRJNA385825 |
| SRA |
SRP106637 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98659_RAW.tar |
240.0 Kb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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