Characterizing transcriptional interference between converging genes in bacteria
- Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-onAntisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two.…
Author details: | Stefan A. HoffmannORCiD, Nan HaoORCiD, Keith E. Shearwin, Katja Maren ArndtORCiDGND |
---|---|
DOI: | https://doi.org/10.1021/acssynbio.8b00477 |
ISSN: | 2161-5063 |
Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/30717589 |
Title of parent work (English): | ACS synthetic biology |
Publisher: | American Chemical Society |
Place of publishing: | Washington |
Publication type: | Article |
Language: | English |
Date of first publication: | 2019/02/05 |
Publication year: | 2019 |
Release date: | 2021/03/24 |
Tag: | Escherichia coli; antisense transcription; gene regulation; mathematical modeling; transcriptional interference |
Volume: | 8 |
Issue: | 3 |
Number of pages: | 15 |
First page: | 466 |
Last Page: | 473 |
Funding institution: | ARCFondation ARC pour la Recherche sur le CancerAustralian Research Council [DE150100091, DP150103009]; CSIRO Synthetic Biology Future Science Platform |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Peer review: | Referiert |