ArticleNature protocols2013
Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components.The EMBO journal · 2024Article
- Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Nuclear dynamics of the Set1C subunit Spp1 prepares meiotic recombination sites for break formation.The Journal of cell biology · 2018Article
- An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking.Bio-protocol · 2018Article
- Software for rapid time dependent ChIP-sequencing analysis (TDCA).BMC bioinformatics · 2017Article
- Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method.Methods (San Diego, Calif.) · 2014Article
- Dynamic regulation of transcriptional states by chromatin and transcription factors.Nature reviews. Genetics · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Competition chromatin immunoprecipitation (competition ChIP) enables experimenters to measure protein-DNA dynamics at a single locus or across the entire genome, depending on the detection method. Competition ChIP relies on a cell containing two copies of a single DNA-associated factor, with each copy of the factor differentially epitope tagged. One of the copies is expressed constitutively and the second is induced as a competitor. The ratio of isoforms associated with discrete genomic locations is detected by ChIP-on-chip (ChIP-chip) or ChIP-sequencing (ChIP-seq). The rate at which the resident isoform of the protein is replaced by the competitor at each binding location enables the calculation of residence time for that factor at each site of interaction genome wide. Here we provide a detailed protocol for designing and performing competition ChIP experiments in Saccharomyces cerevisiae, which takes ∼5 d to complete (not including strain production and characterizations, which may take as long as 6 months). Included in this protocol are guidelines for downstream bioinformatic analysis to extract residence times throughout the genome.
Indexed as
Identifiers
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Registered trials
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.