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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Bibliographic Details
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:
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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
Online Access:Get full text
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Summary: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.
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ISSN:0028-0836
1476-4687
1476-4687
DOI:10.1038/s41586-024-08219-w