ArticleGenome research2011
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 198 papers.
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Who cites it
198 citing papers in PubMed.
- An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activity.PloS one · 2026Article
- Coregulators determine androgen receptor activity in prostate cancer.Bioscience reports · 2025Review
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
- A genetically informed brain atlas for enhancing brain imaging genomics.Nature communications · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 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
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- The characteristics of CTCF binding sequences contribute to enhancer blocking activity.Nucleic acids research · 2024Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.bioRxiv : the preprint server for biology · 2024Article
- Polymerization of ZBTB transcription factors regulates chromatin occupancy.Molecular cell · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.Nature genetics · 2024Article
- Integration of single-cell transcriptome and chromatin accessibility and its application on tumor investigation.Life medicine · 2024Review
- Recapitulation of patient-specific 3D chromatin conformation using machine learning.Cell reports methods · 2023Article
- ChromGene: gene-based modeling of epigenomic data.Genome biology · 2023Article
- Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.Genome biology · 2023Article
- An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping.Nature communications · 2023Article
- Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation.Genome biology · 2023Article
- Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells.BMC bioinformatics · 2022Article
138 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.
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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.