ArticleMolecular cell2014
DNase footprint signatures are dictated by factor dynamics and DNA sequence.
Article in Molecular cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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Who cites it
116 citing papers in PubMed.
- TRiC/CCT chaperonin governs RNA polymerase II activity in the nucleus to support RNA homeostasis.Molecular cell · 2026Article
- NFYB-lncRNA axis resets the tumor microenvironment to promote HCC aggressive progression by a positive feedback loop.Acta pharmaceutica Sinica. B · 2026Article
- Cervicovaginal microbiome alters transcriptomic and chromatin accessibility signatures across cervicovaginal epithelial barriers.Microbiome · 2025Article
- Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling.Nucleic acids research · 2025Article
- 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
- On the identification of differentially-active transcription factors from ATAC-seq data.PLoS computational biology · 2024Article
- On the identification of differentially-active transcription factors from ATAC-seq data.bioRxiv : the preprint server for biology · 2024Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.Briefings in bioinformatics · 2024Review
- Vaginal microbes alter epithelial transcriptome and induce epigenomic modifications providing insight into mechanisms for susceptibility to adverse reproductive outcomes.Research square · 2024Article
- XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency.bioRxiv : the preprint server for biology · 2023Article
- Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.NAR genomics and bioinformatics · 2023Article
- Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation.Genes & development · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation.Nature communications · 2023Article
- Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.Nature communications · 2022Article
- TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile.PLoS computational biology · 2022Article
- 3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin.STAR protocols · 2022Article
56 more citing papers are in PubMed but not listed here.
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Abstract
Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a timescale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor-binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach.
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