ArticleNature methods2014
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
- Two essential criteria for transcription factor footprint discovery using V-plot.Molecular systems biology · 2026Article
- Light-based footprinting of a eukaryotic genome.Science advances · 2026Article
- Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification.ACS chemical biology · 2026Article
- A Cytosine Deaminase-Based Genomic Footprinting Assay (cFOOT-seq) for Detecting Transcription Factor Occupancy.Bio-protocol · 2026Article
- Ryder: Epigenome normalization using a two-tier model and internal reference regions.bioRxiv : the preprint server for biology · 2026Article
- Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo.Genome biology · 2026Article
- COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin.Acta biochimica et biophysica Sinica · 2025Article
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Article
- 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
- Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity.Nature structural & molecular biology · 2025Article
- Review
- Single-cell sequencing to multi-omics: technologies and applications.Biomarker research · 2024Review
- Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.Nucleic acids research · 2024Article
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.Briefings in bioinformatics · 2024Article
- Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.Communications biology · 2024Article
- XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- Single-Cell RNA Sequencing and Its Applications in the Study of Psychiatric Disorders.Biological psychiatry global open science · 2023Review
86 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Sequencing of DNase I hypersensitive sites (DNase-seq) is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize performance of DNase-seq. Sequencing short fragments of 50-100 base pairs (bp) that accumulate in long internucleosome linker regions was more efficient for identifying transcription factor binding sites compared to sequencing longer fragments. We also assessed the potential of DNase-seq to predict transcription factor occupancy via generation of nucleotide-resolution transcription factor footprints. In modeling the sequence-specific DNase I cutting bias, we found a strong effect that varied over more than two orders of magnitude. This indicates that the nucleotide-resolution cleavage patterns at many transcription factor binding sites are derived from intrinsic DNase I cleavage bias rather than from specific protein-DNA interactions. In contrast, quantitative comparison of DNase I hypersensitivity between states can predict transcription factor occupancy associated with particular biological perturbations.
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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.