ArticleNature methods2009
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
Article in Nature methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 380 papers.
What it found
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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.
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Who cites it
380 citing papers in PubMed.
- TRiC/CCT chaperonin governs RNA polymerase II activity in the nucleus to support RNA homeostasis.Molecular cell · 2026Article
- ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.Nucleic acids research · 2026Article
- Light-based footprinting of a eukaryotic genome.Science advances · 2026Article
- NovelbioRxiv : the preprint server for biology · 2026Article
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- A Cytosine Deaminase-Based Genomic Footprinting Assay (cFOOT-seq) for Detecting Transcription Factor Occupancy.Bio-protocol · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- A pipeline for single-cell chromatin accessibility data analysis.Blood science (Baltimore, Md.) · 2026Article
- FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 2025Article
- Deep learning-driven multi-omics analysis: enhancing cancer diagnostics and therapeutics.Briefings in bioinformatics · 2025Review
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Article
- Efficient, scalable, and near-nucleotide-resolution profiling of protein occupancy in the genome with deaminases.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Telomemore enables single-cell analysis of cell cycle and chromatin condensation.Nucleic acids research · 2025Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- 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
- Inferring differential protein binding from time-series chromatin accessibility data.Bioinformatics advances · 2025Article
- Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Single chromatin fiber profiling and nucleosome position mapping in the human brain.Cell reports methods · 2024Article
320 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of eukaryotic genomes. We developed a digital approach to assay regulatory protein occupancy on genomic DNA in vivo by dense mapping of individual DNase I cleavages from intact nuclei using massively parallel DNA sequencing. Analysis of >23 million cleavages across the Saccharomyces cerevisiae genome revealed thousands of protected regulatory protein footprints, enabling de novo derivation of factor binding motifs and the identification of hundreds of new binding sites for major regulators. We observed striking correspondence between single-nucleotide resolution DNase I cleavage patterns and protein-DNA interactions determined by crystallography. The data also yielded a detailed view of larger chromatin features including positioned nucleosomes flanking factor binding regions. Digital genomic footprinting should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.
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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.