ArticleeLife2024
Detection of new pioneer transcription factors as cell-type-specific nucleosome binders.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 15 citations in OpenAlex.
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles.bioRxiv : the preprint server for biology · 2026Article
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- Mechanisms of gene regulation by SRCAP and H2A.Z.Nature communications · 2026Article
- A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nature communications · 2026Article
- GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells.Nature communications · 2025Article
- Genome-wide rules of transcription factor cooperativity revealed throughbioRxiv : the preprint server for biology · 2025Article
- Structural insights into the recognition of native nucleosomes by pioneer transcription factors.Current opinion in structural biology · 2025Review
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- The yin and yang of pioneer transcription factors: Dual roles in repression and activation.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Article
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies.Life (Basel, Switzerland) · 2024Review
- Detection of new pioneer transcription factors as cell-type-specific nucleosome binders.eLife · 2024Article
- Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis.Briefings in bioinformatics · 2024Article
- Identification of mammalian transcription factors that bind to inaccessible chromatin.Nucleic acids research · 2023Article
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Authors and funding
6 authors at 3 institutions in 4 countries.
Funding
Abstract
Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
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