ArticleNature communications2018
Theoretical principles of transcription factor traffic on folded chromatin.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Chromatin organization drives the search mechanism of nuclear factors.Nature communications · 2023Article
- Elastic dosage compensation by X-chromosome upregulation.Nature communications · 2022Article
- First-passage statistics of colloids on fractals: Theory and experimental realization.Science advances · 2022Article
- Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals.Genome biology · 2021Article
- Transcription Factor Dynamics.Cold Spring Harbor perspectives in biology · 2021Review
- Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation.Biophysical journal · 2021Article
- The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes.Biochemical Society transactions · 2021Review
- Article
- 4D nucleome modeling.Current opinion in genetics & development · 2021Review
- Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics.Frontiers in bioinformatics · 2021Article
- Pioneer Transcription Factors Initiating Gene Network Changes.Annual review of genetics · 2020Review
- Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin.Molecular cell · 2020Article
- MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.Genome research · 2020Article
- Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage.Nucleic acids research · 2019Article
- Perichromatin region: a moveable feast.Histochemistry and cell biology · 2018Review
- Signaling by Steroid Hormones in the 3D Nuclear Space.International journal of molecular sciences · 2018Review
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Authors and funding
2 authors.
Funding
Abstract
All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables are known to influence this binding, but the distribution of transcription factor binding patterns remains mostly unexplained in metazoan genomes. Here, we investigate the role of chromosome conformation in the trajectories of transcription factors. Using molecular dynamics simulations, we uncover the principles of their diffusion on chromatin. Chromosome contacts play a conflicting role: at low density they enhance transcription factor traffic, but at high density they lower it by volume exclusion. Consistently, we observe that in human cells, highly occupied targets, where protein binding is promiscuous, are found at sites engaged in chromosome loops within uncompacted chromatin. In summary, we provide a framework for understanding the search trajectories of transcription factors, highlighting the key contribution of genome conformation.
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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.