ArticleJournal of theoretical biology2018
Transcription factor target site search and gene regulation in a background of unspecific binding sites.
Article in Journal of theoretical biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 34 citations in OpenAlex.
- Mechanisms of gene regulation by SRCAP and H2A.Z.Nature communications · 2026Article
- Electrostatic properties of disordered regions control transcription factor search and pioneer activity.Nature communications · 2026Article
- GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion.Nature structural & molecular biology · 2025Article
- Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding.Nature communications · 2025Article
- Dynamic 3D genome reorganization during senescence: defining cell states through chromatin.Cell death and differentiation · 2025Article
- Unveiling the structure and interactions of SOG1, a NAC domain transcription factor: An in-silico perspective.Journal, genetic engineering & biotechnology · 2024Article
- Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.Cell reports · 2023Article
- Article
- Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.Nucleic acids research · 2021Article
- Regulation of transcription reactivation dynamics exiting mitosis.PLoS computational biology · 2021Article
- Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.Nucleic acids research · 2021Article
- Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions.Scientific reports · 2020Article
- Mitotic chromosome binding predicts transcription factor properties in interphase.Nature communications · 2019Article
- GR Dimerization and the Impact of GR Dimerization on GR Protein Stability and Half-Life.Frontiers in immunology · 2019Review
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is accelerated by TF binding to and sliding along unspecific DNA and that unspecific associations alter the occupation frequency of a gene. However, whether target site search time and occupation frequency can be optimized simultaneously is mostly unclear. We developed a transparent and intuitively accessible state-based formalism to calculate search times to target sites on and occupation frequencies of promoters of arbitrary state structure. Our formalism is based on dissociation rate constants experimentally accessible in live cell experiments. To demonstrate our approach, we consider promoters activated by a single TF, by two coactivators or in the presence of a competitive inhibitor. We find that target site search time and promoter occupancy differentially vary with the unspecific dissociation rate constant. Both parameters can be harmonized by adjusting the specific dissociation rate constant of the TF. However, while measured DNA residence times of various eukaryotic TFs correspond to a fast search time, the occupation frequencies of target sites are generally low. Cells might tolerate low target site occupancies as they enable timely gene regulation in response to a changing environment.
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