Chromatin decouples promoter threshold from dynamic range.

Nature
Felix H LamErin K O'Shea

Abstract

Chromatin influences gene expression by restricting access of DNA binding proteins to their cognate sites in the genome. Large-scale characterization of nucleosome positioning in Saccharomyces cerevisiae has revealed a stereotyped promoter organization in which a nucleosome-free region (NFR) is present within several hundred base pairs upstream of the translation start site. Many transcription factors bind within NFRs and nucleate chromatin remodelling events which then expose other cis-regulatory elements. However, it is not clear how transcription-factor binding and chromatin influence quantitative attributes of gene expression. Here we show that nucleosomes function largely to decouple the threshold of induction from dynamic range. With a series of variants of one promoter, we establish that the affinity of exposed binding sites is a primary determinant of the level of physiological stimulus necessary for substantial gene activation, and sites located within nucleosomal regions serve to scale expression once chromatin is remodelled. Furthermore, we find that the S. cerevisiae phosphate response (PHO) pathway exploits these promoter designs to tailor gene expression to different environmental phosphate levels. Our results sug...Continue Reading

References

Aug 1, 1997·The EMBO Journal·T ShimizuT Hakoshima
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Feb 18, 2003·Molecular and Cellular Biology·Joanna A Miller, Jonathan Widom
Jun 25, 2003·Molecular Cell·Hinrich BoegerRoger D Kornberg
Jan 28, 2004·Cell·Sepideh Khorasanizadeh
Dec 2, 2004·Molecular and Cellular Biology·Philipp KorberWolfram Hörz
Mar 16, 2005·Molecular and Cellular Biology·Archana Dhasarathy, Michael P Kladde
Jun 18, 2005·Science·Guo-Cheng YuanOliver J Rando
Jun 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Melissa R Thomas, Erin K O'Shea
Aug 3, 2006·Genes & Development·Jerry L Workman
Jan 16, 2007·Science·Sebastian J Maerkl, Stephen R Quake

❮ Previous
Next ❯

Citations

Jun 10, 2009·Nature Reviews. Genetics·Eran Segal, Jonathan Widom
Jul 10, 2013·Nature Reviews. Genetics·Antoine CoulonDaniel R Larson
Oct 14, 2008·Nature Structural & Molecular Biology·Harold D Kim, Erin K O'Shea
Dec 20, 2011·Nature Structural & Molecular Biology·Nan Hao, Erin K O'Shea
Mar 7, 2013·Nature Structural & Molecular Biology·Kevin Struhl, Eran Segal
Jun 7, 2013·Nature Structural & Molecular Biology·Philipp Tropberger, Robert Schneider
Jun 19, 2013·Nature Structural & Molecular Biology·Manuele CastelnuovoDaniel Zenklusen
Mar 19, 2011·Lab on a Chip·Luis M Fidalgo, Sebastian J Maerkl
May 5, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Kathryn Miller-JensenDavid V Schaffer
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Leonid A Mirny
Aug 15, 2009·The Journal of Biological Chemistry·Lorena Peiró-Chova, Francisco Estruch
Aug 27, 2010·The Journal of Biological Chemistry·Melissa J BlacketerMichael A Shogren-Knaak
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gal Chechik, Daphne Koller
Oct 17, 2009·Briefings in Functional Genomics & Proteomics·Harm van Bakel, Timothy R Hughes
Sep 24, 2010·Nucleic Acids Research·Dong DongZhaolei Zhang
Jan 14, 2012·Nucleic Acids Research·An JansenKevin J Verstrepen
Jul 26, 2011·Nucleic Acids Research·Jason M RizzoMichael J Buck
Aug 21, 2012·Nucleic Acids Research·Elham AslankoohiKevin J Verstrepen
May 20, 2009·Genome Research·Tali Raveh-SadkaEran Segal
Oct 28, 2009·Genome Research·Cédric VaillantAlain Arneodo
Sep 4, 2012·FEMS Yeast Research·Christine L Kerwin, Dennis D Wykoff
May 30, 2009·Science·Marcelo D VincesKevin J Verstrepen
Feb 27, 2010·Science·David Levens, Ashutosh Gupta
Sep 24, 2011·Science·Triantaffyllos GkikopoulosTom Owen-Hughes
Nov 17, 2009·Eukaryotic Cell·Tara M Stanne, Gloria Rudenko
Jun 8, 2011·Microbiology and Molecular Biology Reviews : MMBR·An Jansen, Kevin J Verstrepen
May 31, 2012·Molekuliarnaia biologiia·V B TeĭfV I Krot
Mar 26, 2009·Annual Review of Biochemistry·Oliver J Rando, Howard Y Chang
Jan 10, 2008·Annual Review of Cell and Developmental Biology·Susan E Mango
Nov 10, 2010·BMC Bioinformatics·Fernando Garcia-AlcaldeAdrian J Shepherd

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.