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Structural constraints in collaborative competition of transcription factors against the nucleosome.
Moyle-Heyrman G
,
Tims HS
,
Widom J
.
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Cooperativity in transcription factor (TF) binding is essential in eukaryotic gene regulation and arises through diverse mechanisms. Here, we focus on one mechanism, collaborative competition, which is of interest because it arises both automatically (with no requirement for TF coevolution) and spontaneously (with no requirement for ATP-dependent nucleosome remodeling factors). Previous experimental studies of collaborative competition analyzed cases in which target sites for pairs of cooperating TFs were contained within the same side of the nucleosome. Here, we utilize new assays to measure cooperativity in protein binding to pairs of nucleosomal DNA target sites. We focus on the cases that are of greatest in vivo relevance, in which one binding site is located close to the end of a nucleosome and the other binding site is located at diverse positions throughout the nucleosome. Our results reveal energetically significant positive (favorable) cooperativity for pairs of sites on the same side of the nucleosome but, for the cases examined, energetically insignificant cooperativity between sites on opposite sides of the nucleosome. These findings imply a special significance for TF binding sites that are spaced within one-half nucleosome length (74 bp) or less along the genome and may prove useful for prediction of cooperatively acting TFs genome wide.
Adams,
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative.
1995, Pubmed
Adams,
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative.
1995,
Pubmed
Anderson,
Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites.
2000,
Pubmed
Anderson,
Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation.
2002,
Pubmed
Balaji,
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
2006,
Pubmed
Berman,
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
2004,
Pubmed
Bernstein,
Global nucleosome occupancy in yeast.
2004,
Pubmed
Böhm,
Nucleosome accessibility governed by the dimer/tetramer interface.
2011,
Pubmed
Carey,
The enhanceosome and transcriptional synergy.
1998,
Pubmed
Chávez,
Nucleosome-mediated synergism between transcription factors on the mouse mammary tumor virus promoter.
1997,
Pubmed
Clegg,
Fluorescence resonance energy transfer and nucleic acids.
1992,
Pubmed
Das,
Interacting models of cooperative gene regulation.
2004,
Pubmed
Feng,
Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription.
1993,
Pubmed
Fried,
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis.
1981,
Pubmed
Gansen,
Nucleosome disassembly intermediates characterized by single-molecule FRET.
2009,
Pubmed
Hare,
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation.
2008,
Pubmed
Heinz,
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
2010,
Pubmed
Iqbal,
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids.
2008,
Pubmed
Kao-Huang,
Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: measurement of DNA-bound Escherichia coli lac repressor in vivo.
1977,
Pubmed
Kelbauskas,
Nucleosomal stability and dynamics vary significantly when viewed by internal versus terminal labels.
2008,
Pubmed
Knegtel,
A model for the LexA repressor DNA complex.
1995,
Pubmed
Koopmans,
spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes.
2009,
Pubmed
Levine,
Transcription regulation and animal diversity.
2003,
Pubmed
Li,
Nucleosomes facilitate their own invasion.
2004,
Pubmed
,
Xenbase
Li,
Rapid spontaneous accessibility of nucleosomal DNA.
2005,
Pubmed
Little,
Cleavage of LexA repressor.
1994,
Pubmed
Lowary,
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.
1998,
Pubmed
Miller,
Collaborative competition mechanism for gene activation in vivo.
2003,
Pubmed
Mirny,
Nucleosome-mediated cooperativity between transcription factors.
2010,
Pubmed
Möbius,
Kinetic accessibility of buried DNA sites in nucleosomes.
2006,
Pubmed
Morozov,
Using DNA mechanics to predict in vitro nucleosome positions and formation energies.
2009,
Pubmed
Pilpel,
Identifying regulatory networks by combinatorial analysis of promoter elements.
2001,
Pubmed
Poirier,
Dynamics and function of compact nucleosome arrays.
2009,
Pubmed
Polach,
A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites.
1996,
Pubmed
Polach,
Restriction enzymes as probes of nucleosome stability and dynamics.
1999,
Pubmed
Polach,
Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation.
1995,
Pubmed
Prinsen,
Nucleosome stability and accessibility of its DNA to proteins.
2010,
Pubmed
Raveh-Sadka,
Incorporating nucleosomes into thermodynamic models of transcription regulation.
2009,
Pubmed
Richmond,
The structure of DNA in the nucleosome core.
2003,
Pubmed
Tanaka,
Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo.
1996,
Pubmed
Teif,
Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers.
2011,
Pubmed
Teif,
A lattice model for transcription factor access to nucleosomal DNA.
2010,
Pubmed
Thåström,
Measurement of histone-DNA interaction free energy in nucleosomes.
2004,
Pubmed
Tims,
Stopped-flow fluorescence resonance energy transfer for analysis of nucleosome dynamics.
2007,
Pubmed
Tims,
Dynamics of nucleosome invasion by DNA binding proteins.
2011,
Pubmed
Tirosh,
Two strategies for gene regulation by promoter nucleosomes.
2008,
Pubmed
Vashee,
Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions.
1998,
Pubmed
Vashee,
Synergistic activation of transcription by physiologically unrelated transcription factors through cooperative DNA-binding.
1998,
Pubmed
Wang,
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.
2009,
Pubmed
Widom,
Structure, dynamics, and function of chromatin in vitro.
1998,
Pubmed
Wunderlich,
Different gene regulation strategies revealed by analysis of binding motifs.
2009,
Pubmed
Yang,
FRET-based methods to study ATP-dependent changes in chromatin structure.
2007,
Pubmed
,
Xenbase
Yu,
Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae.
1999,
Pubmed
Yu,
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.
2006,
Pubmed
