A quantitative model of transcription factor–activated gene expression

A challenge facing biology is to develop quantitative, predictive models of gene regulation. Eukaryotic promoters contain transcription factor binding sites of differing affinity and accessibility, but we understand little about how these variables combine to generate a fine-tuned, quantitative transcriptional response. Here we used the PHO5 promoter in budding yeast to quantify the relationship between transcription factor input and gene expression output, termed the gene-regulation function (GRF). A model that captures variable interactions between transcription factors, nucleosomes and the promoter faithfully reproduced the observed quantitative changes in the GRF that occur upon altering the affinity of transcription factor binding sites, and implicates nucleosome-modulated accessibility of transcription factor binding sites in increasing the diversity of gene expression profiles. This work establishes a quantitative framework that can be applied to predict GRFs of other eukaryotic genes.

[1]  W. Hörz,et al.  The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions , 1989, Molecular and cellular biology.

[2]  K. Fascher,et al.  Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication , 1992, Cell.

[3]  J. Schmitz,et al.  A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. , 1994, The EMBO journal.

[4]  M Aldea,et al.  A Set of Vectors with a Tetracycline‐Regulatable Promoter System for Modulated Gene Expression in Saccharomyces cerevisiae , 1997, Yeast.

[5]  Y. Kyōgoku,et al.  Crystal structure of PHO4 bHLH domain–DNA complex: flanking base recognition , 1997, The EMBO journal.

[6]  P. Gregory,et al.  Analyzing chromatin structure and transcription factor binding in yeast. , 1998, Methods.

[7]  M. Münsterkötter,et al.  Cooperative Pho2-Pho4 Interactions at thePHO5 Promoter Are Critical for Binding of Pho4 to UASp1 and for Efficient Transactivation by Pho4 at UASp2 , 1998, Molecular and Cellular Biology.

[8]  E. O’Shea,et al.  Roles of phosphorylation sites in regulating activity of the transcription factor Pho4. , 1999, Science.

[9]  M. T. Hasan,et al.  Exploring the sequence space for tetracycline-dependent transcriptional activators: novel mutations yield expanded range and sensitivity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Applications , 2001, Int. J. High Perform. Comput. Appl..

[11]  Martha S. Cyert,et al.  Regulation of Nuclear Localization during Signaling* , 2001, The Journal of Biological Chemistry.

[12]  E. O’Shea,et al.  Regulation of Chromatin Remodeling by Inositol Polyphosphates , 2002, Science.

[13]  Erin K O'Shea,et al.  Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes , 2003, PLoS biology.

[14]  H. Reinke,et al.  Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. , 2003, Molecular cell.

[15]  J Seth Strattan,et al.  Nucleosomes unfold completely at a transcriptionally active promoter. , 2003, Molecular cell.

[16]  H. Reinke,et al.  Multiple Mechanistically Distinct Functions of SAGA at the PHO5 Promoter , 2003, Molecular and Cellular Biology.

[17]  Mark A Rizzo,et al.  An improved cyan fluorescent protein variant useful for FRET , 2004, Nature Biotechnology.

[18]  J. Tyler,et al.  Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. , 2004, Molecular cell.

[19]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[20]  Jacques Côté,et al.  Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation , 2004, The EMBO journal.

[21]  K. Thorn,et al.  Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae , 2004, Yeast.

[22]  P. Swain,et al.  Gene Regulation at the Single-Cell Level , 2005, Science.

[23]  Hernan G. Garcia,et al.  Transcriptional Regulation by the Numbers 2: Applications , 2004, q-bio/0412011.

[24]  Benjamin B. Kaufmann,et al.  Contributions of low molecule number and chromosomal positioning to stochastic gene expression , 2005, Nature Genetics.

[25]  Archana Dhasarathy,et al.  Promoter Occupancy Is a Major Determinant of Chromatin Remodeling Enzyme Requirements , 2005, Molecular and Cellular Biology.

[26]  J. Tyler,et al.  Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. , 2006, Molecular cell.

[27]  Scott A. Hoose,et al.  Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters , 2006, Nature Structural &Molecular Biology.

[28]  W. Webb,et al.  Dynamics of heat shock factor association with native gene loci in living cells , 2006, Nature.

[29]  T. Kodadek,et al.  Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo , 2006, Nature.

[30]  J. Reese,et al.  Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3 , 2007, Proceedings of the National Academy of Sciences.

[31]  Uri Alon,et al.  Cost–benefit theory and optimal design of gene regulation functions , 2007, Physical biology.

[32]  S. Quake,et al.  A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors , 2007, Science.

[33]  B. Cairns,et al.  Chromatin remodeling: insights and intrigue from single-molecule studies , 2007, Nature Structural &Molecular Biology.

[34]  Jeffrey G. Linger,et al.  Chromatin Disassembly from the PHO5 Promoter Is Essential for the Recruitment of the General Transcription Machinery and Coactivators , 2007, Molecular and Cellular Biology.

[35]  E. O’Shea,et al.  Chromatin decouples promoter threshold from dynamic range , 2008, Nature.

[36]  Roger D. Kornberg,et al.  Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription , 2008, Cell.

[37]  Corentin Spriet,et al.  Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter , 2008, Science.

[38]  E. Segal,et al.  Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.