Single-molecule states link transcription factor binding to gene expression

The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells 1 . However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting 2 , 3...

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Published in:	Nature (London) Vol. 636; no. 8043; pp. 745 - 754
Main Authors:	Doughty, Benjamin R., Hinks, Michaela M., Schaepe, Julia M., Marinov, Georgi K., Thurm, Abby R., Rios-Martinez, Carolina, Parks, Benjamin E., Tan, Yingxuan, Marklund, Emil, Dubocanin, Danilo, Bintu, Lacramioara, Greenleaf, William J.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 19.12.2024 Nature Publishing Group
Subjects:	13 13/106 38 45/15 45/23 45/91 631/208/200 631/337/100 631/337/572 631/553/552 Binding Sites Chromatin DNA - genetics DNA - metabolism DNA Footprinting DNA Methylation Enhancer Elements, Genetic Enhancers Gene expression Gene Expression Regulation Humanities and Social Sciences Humans Interferon Type I - metabolism K562 Cells Kinetics Mammalian cells Models, Molecular multidisciplinary Nucleosomes Nucleosomes - genetics Nucleosomes - metabolism Nucleotide sequence Promoter Regions, Genetic Protein Binding Proteins Regulatory proteins Regulatory sequences Response Elements RNA polymerase Science Science (multidisciplinary) Single Molecule Imaging Statistical mechanics Thermodynamics Transcription factors Transcription Factors - metabolism
ISSN:	0028-0836, 1476-4687, 1476-4687
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Abstract	The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells 1 . However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting 2 , 3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer–promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators. A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor binding contribute to gene expression.
AbstractList	The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer–promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators. The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells 1 . However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting 2 , 3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer–promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators. A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor binding contribute to gene expression. The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells . However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer-promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators. The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells'. However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting2,3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer-promoter constructs with variable numbers of TF binding sites for both a synthetic TF andan endogenous TF involved in the type l interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators. The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells1. However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting2,3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer-promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators.The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells1. However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting2,3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer-promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators.
Author	Doughty, Benjamin R. Marklund, Emil Greenleaf, William J. Schaepe, Julia M. Marinov, Georgi K. Thurm, Abby R. Tan, Yingxuan Parks, Benjamin E. Bintu, Lacramioara Rios-Martinez, Carolina Hinks, Michaela M. Dubocanin, Danilo
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Snippet	The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells 1 . However, the molecular details that link... The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells . However, the molecular details that link... The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells'. However, the molecular details that link... The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells1. However, the molecular details that link... The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells. However, the molecular details that link...
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SubjectTerms	13 13/106 38 45/15 45/23 45/91 631/208/200 631/337/100 631/337/572 631/553/552 Binding Sites Chromatin DNA - genetics DNA - metabolism DNA Footprinting DNA Methylation Enhancer Elements, Genetic Enhancers Gene expression Gene Expression Regulation Humanities and Social Sciences Humans Interferon Type I - metabolism K562 Cells Kinetics Mammalian cells Models, Molecular multidisciplinary Nucleosomes Nucleosomes - genetics Nucleosomes - metabolism Nucleotide sequence Promoter Regions, Genetic Protein Binding Proteins Regulatory proteins Regulatory sequences Response Elements RNA polymerase Science Science (multidisciplinary) Single Molecule Imaging Statistical mechanics Thermodynamics Transcription factors Transcription Factors - metabolism
Title	Single-molecule states link transcription factor binding to gene expression
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