ArticleNature methods2016
Genome-wide footprinting: ready for prime time?
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 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.
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.
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Who cites it
47 citing papers in PubMed, 75 citations in OpenAlex.
- 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
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 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
- ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.Nature communications · 2025Article
- Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.Nature protocols · 2024Review
- Astrocyte allocation during brain development is controlled by Tcf4-mediated fate restriction.The EMBO journal · 2024Article
- Cellular zinc status alters chromatin accessibility and binding of p53 to DNA.Life science alliance · 2024Article
- Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.Briefings in bioinformatics · 2024Review
- Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm.Development (Cambridge, England) · 2024Article
- Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites.bioRxiv : the preprint server for biology · 2023Article
- Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency.bioRxiv : the preprint server for biology · 2023Article
- Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.Nature methods · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- Chromatin accessibility profiling by ATAC-seq.Nature protocols · 2022Review
- Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.Nature cell biology · 2022Article
- A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses.Journal of cell science · 2022Article
- Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB.Scientific reports · 2021Article
- Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia.Nature methods · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput sequencing technologies have allowed many gene locus-level molecular biology assays to become genome-wide profiling methods. DNA-cleaving enzymes such as DNase I have been used to probe accessible chromatin. The accessible regions contain functional regulatory sites, including promoters, insulators and enhancers. Deep sequencing of DNase-seq libraries and computational analysis of the cut profiles have been used to infer protein occupancy in the genome at the nucleotide level, a method introduced as 'digital genomic footprinting'. The approach has been proposed as an attractive alternative to the analysis of transcription factors (TFs) by chromatin immunoprecipitation followed by sequencing (ChIP-seq), and in theory it should overcome antibody issues, poor resolution and batch effects. Recent reports point to limitations of the DNase-based genomic footprinting approach and call into question the scope of detectable protein occupancy, especially for TFs with short-lived chromatin binding. The genomics community is grappling with issues concerning the utility of genomic footprinting and is reassessing the proposed approaches in terms of robust deliverables. Here we summarize the consensus as well as different views emerging from recent reports, and we describe the remaining issues and hurdles for genomic footprinting.
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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.