ArticleNature2018
The interaction landscape between transcription factors and the nucleosome.
Article in Nature, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers.
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Who cites it
236 citing papers in PubMed, 385 citations in OpenAlex.
- Cooperativity enables widespread role of low-affinity motifs in chromatin accessibility and increases regulatory potential.Cell genomics · 2026Article
- A transcription factor by any other name - function beyond DNA binding and transactivation.EMBO reports · 2026Review
- Nucleosomes and IDRs suppress promiscuous GCN4 binding on minichromosomes.Nature structural & molecular biology · 2026Article
- Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.Molecular systems biology · 2026Article
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate.Molecular cell · 2026Article
- Methylation signatures distinguish non-small cell lung cancer subtypes and are associated with survival in smokers with lung squamous cell carcinoma.Journal of the National Cancer Institute · 2026Article
- Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.PLoS computational biology · 2026Article
- Pioneer-factor activity requires stable chromatin occupancy mediated by both sequence-specific binding and disordered protein domains.Science advances · 2026Article
- Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions.Nature communications · 2026Article
- Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome.Acta crystallographica. Section D, Structural biology · 2026Article
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.Nucleic acids research · 2026Article
- Article
- An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors.Developmental biology · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Electrostatic properties of disordered regions control transcription factor search and pioneer activity.Nature communications · 2026Article
176 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 4 institutions in 4 countries.
Funding
Abstract
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.
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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.