ArticleNature methods2014
High-resolution mapping of transcription factor binding sites on native chromatin.
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 119 papers.
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Who cites it
119 citing papers in PubMed, 194 citations in OpenAlex.
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- A role for nucleosome remodellers during resection of deprotected telomeres in yeast.PloS one · 2026Article
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
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- Variations in flanking or less conserved positions of Reb1 and Abf1 consensus binding sites lead to major changes in their ability to modulate nucleosome sliding activity.Biological research · 2025Article
- A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.Genome biology · 2025Article
- Genome-wide maps of UV damage repair and mutation suppression by CPD photolyase.Nucleic acids research · 2025Article
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
- Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.Nature protocols · 2025Review
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.Nature protocols · 2024Review
- H3K4me3 changes occur in cell wall genes during the development ofFrontiers in plant science · 2024Article
- DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins.Nature biotechnology · 2024Article
- Native ChIP: Studying the Genome-Wide Distribution of Histone Modifications in Cells and Tissue.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Functional genomics in Spiralia.Briefings in functional genomics · 2023Article
- Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Research progress of single-cell sequencing in tuberculosis.Frontiers in immunology · 2023Review
59 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. TF profiling is commonly carried out by formaldehyde cross-linking and sonication followed by chromatin immunoprecipitation (X-ChIP). We describe a method to profile TF binding at high resolution without cross-linking. We begin with micrococcal nuclease-digested non-cross-linked chromatin and then perform affinity purification of TFs and paired-end sequencing. The resulting occupied regions of genomes from affinity-purified naturally isolated chromatin (ORGANIC) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide high-resolution maps that are accurate, as defined by the presence of known TF consensus motifs in identified binding sites, that are not biased toward accessible chromatin and that do not require input normalization. We profiled Drosophila melanogaster GAGA factor and Pipsqueak to test ORGANIC performance on larger genomes. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions.
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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.