ArticleNature biotechnology2018
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 40 citations in OpenAlex.
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- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
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- 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
- A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet.International journal of molecular sciences · 2024Article
- Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis.bioRxiv : the preprint server for biology · 2024Article
- TIANA: transcription factors cooperativity inference analysis with neural attention.BMC bioinformatics · 2024Article
- Multiomic profiling of transcription factor binding and function in human brain.Nature neuroscience · 2024Article
- A universal system for boosting gene expression in eukaryotic cell-lines.Nature communications · 2024Article
- Review
- Sea-ATI unravels novel vocabularies of plant active cistrome.Nucleic acids research · 2023Article
- ExplaiNN: interpretable and transparent neural networks for genomics.Genome biology · 2023Article
- PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest.Nature communications · 2022Article
- Characterization of sequence determinants of enhancer function using natural genetic variation.eLife · 2022Article
- WhichTF is functionally important in your open chromatin data?PLoS computational biology · 2022Article
- Sequence determinants of human gene regulatory elements.Nature genetics · 2022Article
- CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.Cell genomics · 2022Article
- Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.Nature cancer · 2021Article
- Improving representations of genomic sequence motifs in convolutional networks with exponential activations.Nature machine intelligence · 2021Article
- Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
No existing method to characterize transcription factor (TF) binding to DNA allows genome-wide measurement of all TF-binding activity in cells. Here we present a massively parallel protein activity assay, active TF identification (ATI), that measures the DNA-binding activity of all TFs in cell or tissue extracts. ATI is based on electrophoretic separation of protein-bound DNA sequences from a highly complex DNA library and subsequent mass-spectrometric identification of the DNA-bound proteins. We applied ATI to four mouse tissues and mouse embryonic stem cells and found that, in a given tissue or cell type, a small set of TFs, which bound to only ∼10 distinct motifs, displayed strong DNA-binding activity. Some of these TFs were found in all cell types, whereas others were specific TFs known to determine cell fate in the analyzed tissue or cell type. We also show that a small number of TFs determined the accessible chromatin landscape of a cell, suggesting that gene regulatory logic may be simpler than previously appreciated.
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