ArticleBiophysical journal2008
Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Article
- Short activation domains control chromatin association of transcription factors.bioRxiv : the preprint server for biology · 2025Article
- Specificity in clustering of gene-specific transcription factors is encoded in the genome.Nucleic acids research · 2025Article
- Exploring focal adhesion data: dynamic parameter extraction from FRAP and FLAP experiments using chemical master equation.Frontiers in molecular biosciences · 2025Article
- A dynamic role for transcription factors in restoring transcription through mitosis.Biochemical Society transactions · 2024Review
- Chromatin organization drives the search mechanism of nuclear factors.Nature communications · 2023Article
- Detecting and quantifying liquid-liquid phase separation in living cells by model-free calibrated half-bleaching.Nature communications · 2022Article
- Review
- Automated modeling of protein accumulation at DNA damage sites using qFADD.py.Biological imaging · 2022Article
- Article
- Intraparticle Kinetics Unveil Crowding and Enzyme Distribution Effects on the Performance of Cofactor-Dependent Heterogeneous Biocatalysts.ACS catalysis · 2021Article
- Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion.Journal of mathematical biology · 2021Article
- DeepFRAP: Fast fluorescence recovery after photobleaching data analysis using deep neural networks.Journal of microscopy · 2021Article
- New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells.Frontiers in cell and developmental biology · 2021Review
- Pioneer Transcription Factors Initiating Gene Network Changes.Annual review of genetics · 2020Review
- Cohesin Removal Reprograms Gene Expression upon Mitotic Entry.Molecular cell · 2020Article
- Isochronal superpositioning in the equilibrium regime of superpressed propylene carbonate to ∼ 1.8 GPa: A study by diffusivity measurement of the fluorescent probe Coumarin 1.The European physical journal. E, Soft matter · 2019Article
- Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions.Nature communications · 2019Article
- Q-FADD: A Mechanistic Approach for Modeling the Accumulation of Proteins at Sites of DNA Damage.Biophysical journal · 2019Article
- A Highly Accurate Pixel-Based FRAP Model Based on Spectral-Domain Numerical Methods.Biophysical journal · 2019Article
44 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
How site-specific transcription factors scan the genome to locate their target sites is a fundamental question in gene regulation. The in vivo binding interactions of several different transcription factors with chromatin have been investigated recently using quantitative fluorescence recovery after photobleaching (FRAP). These analyses have yielded significantly different estimates of both the binding rates and the number of predicted binding states of the respective transcription factors. We show here that these discrepancies are not due to fundamental differences among the site-specific transcription factors, but rather arise from errors in FRAP modeling. The two principal errors are a neglect of diffusion's role and an oversimplified approximation of the photobleach profile. Accounting for these errors by developing a revised FRAP protocol eliminates most of the previous discrepancies in the binding estimates for the three different transcription factors analyzed here. The new estimates predict that for each of the three transcription factors, approximately 75% of the molecules are freely diffusing within the nucleus, whereas the remainder is bound with an average residence time of approximately 2.5 s to a single type of chromatin binding site. Such consistent predictions for three different molecules suggest that many site-specific transcription factors may exhibit similar in vivo interactions with native chromatin.
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