Antisense transcription as a tool to tune gene expression

Molecular Systems Biology
Jennifer A N Brophy, Christopher A Voigt

Abstract

A surprise that has emerged from transcriptomics is the prevalence of genomic antisense transcription, which occurs counter to gene orientation. While frequent, the roles of antisense transcription in regulation are poorly understood. We built a synthetic system in Escherichia coli to study how antisense transcription can change the expression of a gene and tune the response characteristics of a regulatory circuit. We developed a new genetic part that consists of a unidirectional terminator followed by a constitutive antisense promoter and demonstrate that this part represses gene expression proportionally to the antisense promoter strength. Chip-based oligo synthesis was applied to build a large library of 5,668 terminator-promoter combinations that was used to control the expression of three repressors (PhlF, SrpR, and TarA) in a simple genetic circuit (NOT gate). Using the library, we demonstrate that antisense promoters can be used to tune the threshold of a regulatory circuit without impacting other properties of its response function. Finally, we determined the relative contributions of antisense RNA and transcriptional interference to repressing gene expression and introduce a biophysical model to capture the impact of R...Continue Reading

References

Feb 24, 1989·Cell·G J Pruss, K Drlica
May 1, 1994·Journal of Bacteriology·U Vogel, K F Jensen
Aug 1, 1995·Molecular Microbiology·D ViletteB Michel
Jul 1, 1996·Trends in Genetics : TIG·B Dujon
Sep 24, 1999·Journal of Molecular Biology·S LiangH Bremer
Dec 2, 2000·Nature Biotechnology·D W SelingerG M Church
Apr 27, 2002·Journal of Bacteriology·Sabine Brantl, E Gerhart H Wagner
Nov 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yohei YokobayashiFrances H Arnold
Mar 18, 2003·Nature Biotechnology·Rodrigo YelinGalit Rotman
May 6, 2003·Science·Vitaly Epshtein, Evgeny Nudler
Sep 13, 2003·The EMBO Journal·Vitaly EpshteinEvgeny Nudler
Sep 19, 2003·Current Biology : CB·Daniel L Kaplan, Mike O'Donnell
Apr 6, 2004·Current Opinion in Microbiology·Jeffrey Roberts, Joo-Seop Park
Dec 24, 2004·Nature·Jingdong TianGeorge Church
Jan 27, 2005·Journal of Molecular Biology·Kim SneppenJ Barry Egan
Jun 1, 2005·Trends in Genetics : TIG·Keith E ShearwinJ Barry Egan
Jun 3, 2005·Genome Research·Morgan N PriceEric J Alm
Nov 2, 2005·Nucleic Acids Research·Mitsuoki KawanoRobert G Martin
Feb 14, 2006·Current Protein & Peptide Science·F SaïdaF Bontems
Nov 18, 2006·Cell·Cintia F HongayGerald R Fink
Mar 28, 2007·Current Opinion in Microbiology·Sabine Brantl
Mar 31, 2007·Current Opinion in Microbiology·Richard G Brennan, Todd M Link
Apr 28, 2007·Molecular Microbiology·Mitsuoki KawanoGisela Storz
Jul 20, 2007·Journal of Bioinformatics and Computational Biology·Maria N TutukinaOlga N Ozoline
Nov 16, 2007·Molecular Systems Biology·Robert Sidney CoxMichael B Elowitz
Aug 5, 1997·Biotechnology and Bioengineering·T A Carrier, J D Keasling
Dec 5, 2008·Microbiology and Molecular Biology Reviews : MMBR·Elizabeth M FozoGisela Storz
Dec 6, 2008·Science·Yiping HeKenneth W Kinzler
May 21, 2009·Molecular Systems Biology·Nicolas E Buchler, Frederick R Cross
Sep 17, 2009·Molecular Systems Biology·Jens GeorgWolfgang R Hess
Oct 6, 2009·Nature Biotechnology·Howard M SalisChristopher A Voigt
Nov 4, 2009·Genome Research·Omri WurtzelRotem Sorek
Dec 8, 2009·Science·Marc GüellLuis Serrano
Feb 5, 2010·Nucleic Acids Research·Mara GiangrossiMaurizio Falconi
Mar 2, 2010·Journal of Bacteriology·Melanie J FiliatraultDavid J Schneider
Mar 10, 2010·Nucleic Acids Research·Kevin F MurphyJames J Collins
Apr 20, 2010·Molecular Microbiology·Eun-Jin Lee, Eduardo A Groisman
Jun 22, 2010·Nature·Paula Montero LlopisChristine Jacobs-Wagner

❮ Previous
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Citations

Jun 28, 2016·ACS Synthetic Biology·Antoni E BordoyAnushree Chatterjee
Oct 19, 2016·Current Opinion in Microbiology·Robert W BradleyBaojun Wang
Oct 6, 2016·Biotechnology Letters·Irem Avcilar-Kucukgoze, Zoya Ignatova
Nov 3, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Aditya Kumar, Manju Bansal
Jan 5, 2017·Cold Spring Harbor Perspectives in Biology·Randall A Hughes, Andrew D Ellington
Jun 8, 2017·Integrative Biology : Quantitative Biosciences From Nano to Macro·Kevin A JanesDouglas A Lauffenburger
Jun 14, 2017·Nucleic Acids Research·Amar Ghodasara, Christopher A Voigt
May 17, 2018·Phytopathology·Domenico AbateFrancesco Faretra
Mar 10, 2018·Molecular Systems Biology·Antoine VigourouxSven van Teeffelen
Nov 11, 2017·Molecular Systems Biology·Thomas E GorochowskiChristopher A Voigt
May 17, 2019·Plant & Cell Physiology·Elvira Olmedo-VerdAlicia M Muro-Pastor
Oct 5, 2019·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Maggie HicksBaojun Wang
Mar 7, 2020·Molecular Systems Biology·Jonghyeon ShinChristopher A Voigt
Feb 23, 2020·FEMS Microbiology Reviews·S Joke LambrechtWolfgang R Hess
Oct 9, 2019·Nature Biotechnology·Alexander C ReisHoward M Salis
Aug 20, 2020·Molecular Systems Biology·Yongjin ParkChristopher A Voigt
Sep 24, 2019·Nucleic Acids Research·Natalia BargerRamez Daniel
Sep 15, 2020·Frontiers in Molecular Biosciences·Zachary ArdernSiegfried Scherer
Sep 9, 2020·Nature Chemical Biology·Xianhao XuLong Liu
Oct 27, 2017·Frontiers in Computational Neuroscience·Lingli Zhou, Jianwei Shen
Jan 25, 2020·Nature Communications·Timothy T HardenJeff Gelles
Apr 20, 2018·Nature Communications·Avihu H YonaJeff Gore
Mar 15, 2018·Frontiers in Microbiology·Stephen C HeinschMichael J Smanski
Oct 7, 2020·Nature Communications·Amin Espah BorujeniChristopher A Voigt
Mar 10, 2020·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Philip P Adams, Gisela Storz
Mar 13, 2021·ACS Synthetic Biology·Nolan J O'ConnorAnushree Chatterjee
Oct 4, 2020·Molecular Cell·Thijs NieuwkoopNico J Claassens
May 25, 2021·Research in Microbiology·Kesia Esther da SilvaSimone Simionatto
Jun 4, 2021·Communications Biology·Jayan RammohanDavid Ross
May 20, 2021·Nucleic Acids Research·Phyana LitovcoRamez Daniel
Jun 26, 2021·Microbial Biotechnology·Lisa Tietze, Rahmi Lale
Jul 14, 2018·Microbiology Spectrum·Jens Georg, Wolfgang R Hess
Jan 23, 2019·ACS Synthetic Biology·Balwina KoopalJohn van der Oost
Sep 19, 2019·ACS Synthetic Biology·Antoni E BordoyAnushree Chatterjee
Feb 6, 2019·ACS Synthetic Biology·Stefan A HoffmannKatja M Arndt
May 5, 2021·Genome Biology and Evolution·Martijn CallensStéphanie Bedhomme

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Datasets Mentioned

BETA
SRP065456

Methods Mentioned

BETA
Fluorescence
flow cytometry
PCR
electrophoresis

Software Mentioned

IlluminaSeqAnalysis . m
MATLAB
TarA
bvp4c
MATLAB function bvpinit
IlluminaEnrichmentGrid . m
FlowJo
IlluminaPerfSeqAnalysis . m

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