ArticleNature biotechnology2014
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.
Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 272 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
272 citing papers in PubMed.
- A chromatin-informed transcriptional regulatory framework to stratify patients and guide therapy selection in triple-negative breast cancer.Nature communications · 2026Article
- Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction.NAR genomics and bioinformatics · 2026Article
- Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice.The EMBO journal · 2026Article
- Age-independent and targetable transcription factor networks regulating CD8Cell reports · 2026Article
- A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.Nucleic acids research · 2026Article
- Oncogenic virus hijacks SOX18 pioneer function to enhance viral persistence.Research square · 2025Article
- Molecular Determinants of the Human Retinal Pigment Epithelium Cell Fate and Potential Pharmacogenomic Targets for Precision Medicine.International journal of molecular sciences · 2025Article
- Base editing of trinucleotide repeats that cause Huntington's disease and Friedreich's ataxia reduces somatic repeat expansions in patient cells and in mice.Nature genetics · 2025Article
- OLIG2 mediates a rare targetable stem cell fate transition in sonic hedgehog medulloblastoma.Nature communications · 2025Article
- The role(s) of NF-Y in development and differentiation.Cell death and differentiation · 2025Review
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Genome access is transcription factor-specific and defined by nucleosome position.Molecular cell · 2024Article
- Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data.Cell systems · 2024Article
- Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional and epigenetic characterization of a new in vitro platform to model the formation of human pharyngeal endoderm.Genome biology · 2024Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.Genome biology · 2024Article
- Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids.Nature communications · 2024Article
- RNA polymerase II promotes the organization of chromatin following DNA replication.EMBO reports · 2024Article
212 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
9 authors.
Funding
Abstract
We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.
Indexed as
Identifiers
What OpenQuestion holds
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.