Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity

Biological Reviews of the Cambridge Philosophical Society
Yaolai WangFeng Liu

Abstract

There is accumulating evidence that, from bacteria to mammalian cells, messenger RNAs (mRNAs) are produced in intermittent bursts - a much 'noisier' process than traditionally thought. Based on quantitative measurements at individual promoters, diverse phenomenological models have been proposed for transcriptional bursting. Nevertheless, the underlying molecular mechanisms and significance for cellular signalling remain elusive. Here, we review recent progress, address the above issues and illuminate our viewpoints with simulation results. Despite being widely used in modelling and in interpreting experimental data, the traditional two-state model is far from adequate to describe or infer the molecular basis and stochastic principles of transcription. In bacteria, DNA supercoiling contributes to the bursting of those genes that express at high levels and are topologically constrained in short loops; moreover, low-affinity cis-regulatory elements and unstable protein complexes can play a key role in transcriptional regulation. Integrating data on the architecture, kinetics, and transcriptional input-output function is a promising approach to uncovering the underlying dynamic mechanism. For eukaryotes, distinct bursting features ...Continue Reading

References

May 1, 1992·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·M S Ko
Nov 11, 1998·Molecular Cell·E BertrandR M Long
Feb 2, 2002·Science·Ali H Brivanlou, James E Darnell
Oct 5, 2002·Nucleic Acids Research·Francis Lim, David S Peabody
Apr 11, 2003·Nature·William J BlakeJ J Collins
Apr 29, 2004·Nature Structural & Molecular Biology·Steven Hahn
May 18, 2005·Trends in Biochemical Sciences·Roger D Kornberg
May 18, 2005·Trends in Biochemical Sciences·Sohail Malik, Robert G Roeder
Dec 20, 2005·Cell·Ido GoldingEdward C Cox
May 23, 2006·Current Biology : CB·Jonathan R ChubbRobert H Singer
May 23, 2006·Nature Structural & Molecular Biology·Frédéric CatezMichael Bustin
Jul 25, 2006·Critical Reviews in Biochemistry and Molecular Biology·Mary C Thomas, Cheng-Ming Chiang
Oct 20, 2006·PLoS Biology·Arjun RajSanjay Tyagi
Feb 27, 2007·Cell·Tony Kouzarides
Jul 17, 2007·Cell·Thomas GregorWilliam Bialek
Aug 3, 2007·Proceedings of the National Academy of Sciences of the United States of America·Roger D Kornberg
Jan 19, 2008·Science·Juan M Pedraza, Johan Paulsson
Oct 30, 2008·Cell·Arjun Raj, Alexander van Oudenaarden
Sep 29, 2009·Molecular Cell·Gordon L HagerTom Misteli
Apr 28, 2010·Nature Reviews. Genetics·Vikki M Weake, Jerry L Workman
Jul 20, 2010·Current Opinion in Genetics & Development·Jonathan R Chubb, Tanniemola B Liverpool
Sep 11, 2010·Nature·Avigdor Eldar, Michael B Elowitz
May 3, 2011·Nature Genetics·Lok-Hang SoIdo Golding
Sep 3, 2011·Science·Christopher S Nabel, Rahul M Kohli
Feb 22, 2012·Cell·Richard L Gourse, Robert Landick
Mar 14, 2012·EMBO Reports·Timothée Lionnet, Robert H Singer
Apr 14, 2012·Science·Brian MunskyAlexander van Oudenaarden
Oct 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Roy D DarLeor S Weinberger
Mar 26, 2013·Nature Methods·J Christof M GebhardtX Sunney Xie
Apr 6, 2013·Methods : a Companion to Methods in Enzymology·Alvaro SanchezJane Kondev
May 31, 2013·Proceedings of the National Academy of Sciences of the United States of America·Larry J FriedmanJeff Gelles
Jun 15, 2013·Nature Protocols·Colin R LickwarJason D Lieb

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Citations

Mar 4, 2020·Nucleic Acids Research·Haitham A Shaban, Andrew Seeber
Jul 23, 2020·G3 : Genes - Genomes - Genetics·Eyal Metzl-RazNaama Barkai
Dec 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Adam J NorthcuttDavid J Schulz
Jan 8, 2020·International Journal of Molecular Sciences·Jekaterina Erenpreisa, Alessandro Giuliani
Nov 27, 2020·Current Opinion in Cell Biology·Nicholas C LammersHernan G Garcia
Dec 4, 2021·Proceedings of the National Academy of Sciences of the United States of America·Kenneth WuRohinton T Kamakaka

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Methods Mentioned

BETA
fluorescence microscopy

Software Mentioned

R

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