ArticleNucleic acids research2008
Spatial effects on the speed and reliability of protein-DNA search.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Mechanisms of search for specific sites in DNA by DNA-binding proteins.Biochemistry and biophysics reports · 2026Review
- Article
- Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids.Nature communications · 2024Article
- Article
- Protein-DNA recognition mechanisms and specificity.Biophysical reviews · 2023Review
- The molecular grammar of protein disorder guiding genome-binding locations.Nucleic acids research · 2023Article
- Article
- The economy of chromosomal distances in bacterial gene regulation.NPJ systems biology and applications · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
- Argonaute bypasses cellular obstacles without hindrance during target search.Nature communications · 2019Article
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions.Nucleic acids research · 2019Article
- Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation.Chemical reviews · 2018Review
- Protein motion in the nucleus: from anomalous diffusion to weak interactions.Biochemical Society transactions · 2018Review
- Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks.Biophysical journal · 2018Article
- The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation.Scientific reports · 2017Article
- Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion.PLoS computational biology · 2016Article
- Facilitated diffusion buffers noise in gene expression.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Physical constraints determine the logic of bacterial promoter architectures.Nucleic acids research · 2014Article
- Quantitative influence of macromolecular crowding on gene regulation kinetics.Nucleic acids research · 2014Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Strong experimental and theoretical evidence shows that transcription factors (TFs) and other specific DNA-binding proteins find their sites using a two-mode search: alternating between three-dimensional (3D) diffusion through the cell and one-dimensional (1D) sliding along the DNA. We show that, due to the 1D component of the search process, the search time of a TF can depend on the initial position of the TF. We formalize this effect by discriminating between two types of searches: global and local. Using analytical calculations and simulations, we estimate how close a TF and binding site need to be to make a local search likely. We then use our model to interpret the wide range of experimental measurements of this parameter. We also show that local and global searches differ significantly in average search time and the variability of search time. These results lead to a number of biological implications, including suggestions of how prokaryotes achieve rapid gene regulation and the relationship between the search mechanism and noise in gene expression. Lastly, we propose a number of experiments to verify the existence and quantify the extent of spatial effects on the TF search process in prokaryotes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.