TATA is a modular component of synthetic promoters.

Genome Research
Ilaria MognoBarak A Cohen

Abstract

The expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docking site for the RNA polymerase holoenzyme. Using a synthetic promoter system coupled to a thermodynamic model of combinatorial regulation, we analyze the effects of different strength TATA boxes on various aspects of combinatorial cis-regulation. The thermodynamic model explains 75% of the variance in gene expression in synthetic promoter libraries with different strength TATA boxes, suggesting that many of the salient aspects of cis-regulation are captured by the model. Our results demonstrate that the effect of changing the TATA box on gene expression is the same for all synthetic promoters regardless of the arrangement of cis-regulatory sites we studied. Our analysis also showed that in our synthetic system the strength of the RNA polymerase-TATA interaction does not alter the combinatorial interactions between transcription factors, or between transcription factors and RNA polymerase. Finally, we show that alth...Continue Reading

References

Jan 20, 1985·Journal of Molecular Biology·M A Shea, G K Ackers
Jan 1, 1995·Annual Review of Genetics·K Struhl
Oct 21, 2000·Genes & Development·B Lemon, R Tjian
Jun 13, 2001·The Journal of Biological Chemistry·J J Stewart, L A Stargell
Jan 30, 2004·Nature·Johan Paulsson
Mar 10, 2004·Cell·Andrew D BasehoarB Franklin Pugh
May 29, 2004·Science·Jonathan M Raser, Erin K O'Shea
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Mar 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Sorin Istrail, Eric H Davidson
Mar 31, 2005·Current Opinion in Genetics & Development·Lacramioara BintuRob Phillips
Apr 16, 2005·Molecular and Cellular Biology·Meghana M Kulkarni, David N Arnosti
Dec 24, 2005·Nature·Dmitri VolfsonJeff Hasty
Jan 18, 2006·Genetics·Martin LigrEric D Siggia
May 23, 2006·Nature Genetics·Arren Bar-EvenNaama Barkai
Jun 20, 2006·Nature Genetics·Itay TiroshNaama Barkai
Dec 26, 2006·Molecular Cell·William J BlakeJames J Collins
Feb 24, 2007·Current Opinion in Genetics & Development·Benjamin B Kaufmann, Alexander van Oudenaarden
Jul 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kevin F MurphyJames J Collins
Jul 27, 2007·PloS One·Timothy H-C HsiauJoseph C Corbo
Nov 6, 2007·Cell·Iftach NachmanSharad Ramanathan
Nov 16, 2007·Molecular Systems Biology·Robert Sidney CoxMichael B Elowitz
Jul 18, 2008·Nature·Jan M SkotheimFrederick R Cross
Feb 20, 2009·Molecular Systems Biology·Jason Gertz, Barak A Cohen
Sep 22, 2009·Nature Structural & Molecular Biology·Folkert J van WervenH Th Marc Timmers

❮ Previous
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Citations

Aug 21, 2013·Nature Genetics·Arun S RajkumarSebastian J Maerkl
Jul 24, 2012·Genome Research·Gil HornungNaama Barkai
Jul 26, 2014·PloS One·Francesco Luigi Massimo VallaniaRobi David Mitra
May 9, 2014·PLoS Computational Biology·Marc S Sherman, Barak A Cohen
Jun 11, 2014·Nature Reviews. Genetics·Michal Levo, Eran Segal
Nov 20, 2014·Epigenetics & Chromatin·Lisette C M Anink-GroenenFrank J Bruggeman
May 10, 2013·ACS Synthetic Biology·Arun S Rajkumar, Sebastian J Maerkl
Aug 21, 2018·ELife·Fabien DuveauPatricia J Wittkopp
Jun 30, 2016·Scientific Reports·Zhiming DaiXianhua Dai
Apr 12, 2019·Briefings in Bioinformatics·Saman ZeeshanZeeshan Ahmed
Dec 15, 2010·Protein & Cell·Hong Zhang, Taijiao Jiang
Jun 2, 2018·Molecular Biotechnology·Jameel AyshaXiaowei Li
Jun 18, 2016·Genome Research·Thomas A NguyenJesse M Gray
Jul 22, 2017·Plant Molecular Biology·Gillian H DeanGeorge W Haughn
Jul 15, 2017·Science Advances·Antoine BaudrimontAttila Becskei
Aug 13, 2020·Metabolites·Hongting TangJay D Keasling
Feb 23, 2020·International Journal of Molecular Sciences·Aysha JameelHaiyan Li
Jun 3, 2021·International Journal of Molecular Sciences·Xiaofan Feng, Mario Andrea Marchisio
Dec 16, 2016·ACS Synthetic Biology·Rui M C PortelaAnton Glieder
May 15, 2015·Genome Research·Shai LublinerEran Segal

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