Document Detail


Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.
MedLine Citation:
PMID:  23764940     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Colin R Lickwar; Florian Mueller; Jason D Lieb
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2013-06-13
Journal Detail:
Title:  Nature protocols     Volume:  8     ISSN:  1750-2799     ISO Abbreviation:  Nat Protoc     Publication Date:  2013  
Date Detail:
Created Date:  2013-06-14     Completed Date:  2014-01-14     Revised Date:  2014-07-14    
Medline Journal Info:
Nlm Unique ID:  101284307     Medline TA:  Nat Protoc     Country:  England    
Other Details:
Languages:  eng     Pagination:  1337-53     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Binding Sites
Chromatin Immunoprecipitation / methods*
DNA / analysis,  metabolism*
Epitopes
Genome
Protein Binding
Protein Isoforms / genetics,  metabolism
Proteins / analysis*,  metabolism*
Saccharomyces cerevisiae / genetics,  metabolism
Single-Cell Analysis / methods
Grant Support
ID/Acronym/Agency:
R01 GM072518/GM/NIGMS NIH HHS; T32 GM007092/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Epitopes; 0/Protein Isoforms; 0/Proteins; 9007-49-2/DNA

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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