ArticleDevelopmental cell2023
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.
Article in Developmental cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Enhancer binding kinetics explain transcription factor hub formation.Science advances · 2026Article
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
- AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026Article
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Asymmetric chromatin accessibility underlies anterior-posterior axis specification in moth fly embryos.PLoS biology · 2026Article
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- Article
- Altered AP-1, RUNX, and EGR chromatin dynamics drive human fibrotic lung disease.Annals of the rheumatic diseases · 2026Article
- YAP Induces a Prorenewal Metabolic State in Cardiomyocytes.Circulation · 2026Article
- FOSL2 regulates endothelial cell state and chromatin accessibility in systemic sclerosis pulmonary vascular remodeling.JCI insight · 2026Article
- Chromatin Accessibility in Cancer: Biological Functions, Mechanisms, Therapeutic Potential, and Future Directions.MedComm · 2026Review
- Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters.Science advances · 2026Article
- Review
- The functional organization of chromosome territories in single nuclei during zygotic genome activation.Scientific reports · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- Refining sequence-to-activity models by increasing model resolution.Bioinformatics advances · 2026Article
- Cooperation between architectural C2H2 proteins in CP190 recruitment to Drosophila regulatory elements.Epigenetics & chromatin · 2025Article
- Post-transcriptional suppression of the pioneer factor Zelda protects the adult Drosophila testis from activation of the ovary program.PLoS biology · 2025Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores.bioRxiv : the preprint server for biology · 2025Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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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.