ArticleGenome research2019
Defining TP53 pioneering capabilities with competitive nucleosome binding assays.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 64 citations in OpenAlex.
- Evaluating high-fidelity CRISPR-Cas nucleases in nucleosomal contexts using a quantitative framework.Frontiers in genome editing · 2026Article
- AP1 is a pioneer transcription factor that programmes cell fate through MADS-domain protein tetramerisation.Genome biology · 2025Article
- DNA bendability regulates transcription factor binding to nucleosomes.Nature structural & molecular biology · 2025Article
- Defining transcription factor nucleosome binding with Pioneer-seq.PLoS genetics · 2025Article
- p53 reveals principles of chromatin remodeling and enhancer activation.Nucleic acids research · 2025Article
- Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites.Genome research · 2025Article
- p53motifDB: integration of genomic information and tumour suppressor p53 binding motifs.Database : the journal of biological databases and curation · 2025Article
- Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns.Nature communications · 2024Article
- Determinants of p53 DNA binding, gene regulation, and cell fate decisions.Cell death and differentiation · 2024Review
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Pioneer factors - key regulators of chromatin and gene expression.Nature reviews. Genetics · 2023Article
- Chromatin organization drives the search mechanism of nuclear factors.Nature communications · 2023Article
- Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nature communications · 2023Article
- Chromatin structure related to oncogenesis.Cancer science · 2023Review
- The impact of nucleosome structure on CRISPR/Cas9 fidelity.Nucleic acids research · 2023Article
- A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1.Genome biology · 2022Article
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- Structures and consequences of pioneer factor binding to nucleosomes.Current opinion in structural biology · 2022Review
- Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model.Nature communications · 2022Article
- Article
Corrections and comments
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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
Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a TF binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest TP53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how TP53 binds to nucleosomal DNA. To comprehensively examine TP53 nucleosome binding, we competitively bound TP53 to multiple in vitro-formed nucleosomes containing a high- or low-affinity TP53 TFBS located at differing translational and rotational positions within the nucleosome. Stable TP53-nucleosome complexes were isolated and quantified using next-generation sequencing. Our results demonstrate TP53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Binding site affinity only affects TP53 binding for TFBSs located at the same nucleosomal positions; otherwise, nucleosome position takes precedence. Furthermore, TP53 has strong nonspecific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining TP53-induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome-free region. Overall, our results suggest that the pioneering capabilities of TP53 are driven by nonspecific nucleosome binding with specific binding at nucleosome edges.
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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.