ArticleProceedings of the National Academy of Sciences of the United States of America2020
Nucleosome allostery in pioneer transcription factor binding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 96 citations in OpenAlex.
- Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate.Molecular cell · 2026Article
- H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.Nucleic acids research · 2026Article
- SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.eLife · 2026Article
- Zinc-finger transcription factor Fzf1 binds to its target DNA in a non-canonical manner.Nucleic acids research · 2026Article
- GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion.Nature structural & molecular biology · 2025Article
- Defining transcription factor nucleosome binding with Pioneer-seq.PLoS genetics · 2025Article
- Article
- Post-translational modification of transcription factors: perspectives in vascular medicine.Cell death & disease · 2025Review
- Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations.Biophysical journal · 2025Article
- Interfacial water confers transcription factors with dinucleotide specificity.Nature structural & molecular biology · 2025Article
- Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion.PLoS computational biology · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.Nature structural & molecular biology · 2024Article
- GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.Nature communications · 2024Article
- Pioneer factors: roles and their regulation in development.Trends in genetics : TIG · 2024Review
- Detection of new pioneer transcription factors as cell-type-specific nucleosome binders.eLife · 2024Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While recent experiments revealed that some pioneer transcription factors (TFs) can bind to their target DNA sequences inside a nucleosome, the binding dynamics of their target recognitions are poorly understood. Here we used the latest coarse-grained models and molecular dynamics simulations to study the nucleosome-binding procedure of the two pioneer TFs, Sox2 and Oct4. In the simulations for a strongly positioning nucleosome, Sox2 selected its target DNA sequence only when the target was exposed. Otherwise, Sox2 entropically bound to the dyad region nonspecifically. In contrast, Oct4 plastically bound on the nucleosome mainly in two ways. First, the two POU domains of Oct4 separately bound to the two parallel gyres of the nucleosomal DNA, supporting the previous experimental results of the partial motif recognition. Second, the POU
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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.