In vitro binding energies capture Klf4 occupancy across the human genome
4 affiliations
- 1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- 2Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
- 3Cluster of Excellence Physics of Life, Technical University Dresden, Dresden 01062, Germany
- 4Center for Systems Biology Dresden, Dresden 01307, Germany
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific genomic loci determined by DNA sequence. Their sequence specificity is commonly summarized by a consensus binding motif. However, eukaryotic genomes contain billions of low-affinity DNA sequences to which TFs associate with a sequence-dependent binding energy. We currently lack insight into how the genomic sequence defines this spectrum of binding energies and the resulting pattern of TF localization. Here, we set out to obtain a quantitative understanding of sequence-dependent TF binding to both motif and nonmotif sequences. We achieve this by first pursuing accurate measurements of physical binding energies of human TF Krüppel-like factor 4 (Klf4) to a library of short DNA sequences in a fluorescence-anisotropy-based bulk competitive binding assay. Second, we show that the highly nonlinear sequence dependence of Klf4 binding energies can be captured by combining a linear model of binding energies with an Ising model of the coupled recognition of nucleotides by a TF. In this model, nucleotide–TF interfaces collectively switch between two states, weak binding and strong nucleotide-specific binding, and the states of neighboring interfaces are coupled with J∼2kBT. We find that this statistical mechanics model parameterized by our in vitro measurements captures Klf4 binding patterns on an individual long DNA molecule stretched in the optical tweezer, and is predictive for Klf4 occupancy across the entire human genome without additional fit parameters.
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BibTeX
@article{schwager2026vitro,
title = {{In vitro binding energies capture Klf4 occupancy across the human genome}},
author = {Anne Schwager and Jonas Neipel and Yahor Savich and Douglas Diehl and Frank Jülicher and Anthony A. Hyman and Stephan W. Grill},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = oct,
doi = {10.1073/pnas.2538133123},
url = {https://doi.org/10.1073/pnas.2538133123},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - In vitro binding energies capture Klf4 occupancy across the human genome
AU - Anne Schwager
AU - Jonas Neipel
AU - Yahor Savich
AU - Douglas Diehl
AU - Frank Jülicher
AU - Anthony A. Hyman
AU - Stephan W. Grill
PY - 2026
DA - 2026/10/26
JO - Proceedings of the National Academy of Sciences of the United States of America
DO - 10.1073/pnas.2538133123
UR - https://doi.org/10.1073/pnas.2538133123
AB - Transcription factors (TFs) regulate gene expression by binding to specific genomic loci determined by DNA sequence. Their sequence specificity is commonly summarized by a consensus binding motif. However, eukaryotic genomes contain billions of low-affinity DNA sequences to which TFs associate with a sequence-dependent binding energy. We currently lack insight into how the genomic sequence defines this spectrum of binding energies and the resulting pattern of TF localization. Here, we set out to obtain a quantitative understanding of sequence-dependent TF binding to both motif and nonmotif sequences. We achieve this by first pursuing accurate measurements of physical binding energies of human TF Krüppel-like factor 4 (Klf4) to a library of short DNA sequences in a fluorescence-anisotropy-based bulk competitive binding assay. Second, we show that the highly nonlinear sequence dependence of Klf4 binding energies can be captured by combining a linear model of binding energies with an Ising model of the coupled recognition of nucleotides by a TF. In this model, nucleotide–TF interfaces collectively switch between two states, weak binding and strong nucleotide-specific binding, and the states of neighboring interfaces are coupled with J∼2kBT. We find that this statistical mechanics model parameterized by our in vitro measurements captures Klf4 binding patterns on an individual long DNA molecule stretched in the optical tweezer, and is predictive for Klf4 occupancy across the entire human genome without additional fit parameters.
SN - 0027-8424
SN - 1091-6490
ER -