| ChIP-exo Method for Identifying Genomic Location of DNA-Binding Proteins with Near-Single-Nucleotide Accuracy. | |
| | |
MedLine Citation:
|
PMID: 23026909 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
|
This unit describes the ChIP-exo methodology, which combines chromatin immunoprecipitation (ChIP) with lambda exonuclease digestion followed by high-throughput sequencing. ChIP-exo allows identification of a nearly complete set of the binding locations of DNA-binding proteins at near-single-nucleotide resolution with almost no background. The process is initiated by cross-linking DNA and associated proteins. Chromatin is then isolated from nuclei and subjected to sonication. Subsequently, an antibody against the desired protein is used to immunoprecipitate specific DNA-protein complexes. ChIP DNA is purified, sequencing adaptors are ligated, and the adaptor-ligated DNA is then digested by lambda exonuclease, generating 25- to 50-nucleotide fragments for high-throughput sequencing. The sequences of the fragments are mapped back to the reference genome to determine the binding locations. The 5' ends of DNA fragments on the forward and reverse strands indicate the left and right boundaries of the DNA-protein binding regions, respectively. Curr. Protoc. Mol. Biol. 100:21.24.1-21.24.14. © 2012 by John Wiley & Sons, Inc. |
| | |
Authors:
|
Ho Sung Rhee; B Franklin Pugh |
Related Documents
:
|
3924429 - Studies on the detoxication of microsomally-activated aflatoxin b1 by glutathione and g... 1165469 - Synthesis and degradation of ribosomal rna in regenerating liver. 16440339 - Deoxyribonuclease 1 aggravates acetaminophen-induced liver necrosis in male cd-1 mice. 6168289 - Liver and kidney nuclear rna synthesis and modifications in dimethylnitrosamine-treated... 804349 - A comparison of the effects of 3'-methyl-4-dimethylaminoazobenzene, 2-methyl-4-dimethyl... 10694929 - Evidence of 14c-furazolidone metabolite binding to the hepatic dna of trout. 11968009 - Evidence that protein disulfide isomerase (pdi) is involved in dna-nuclear matrix ancho... 2461219 - Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline c... 17172419 - Fanconi anemia d2 protein confers chemoresistance in response to the anticancer agent, ... |
Publication Detail:
|
Type: Journal Article |
Journal Detail:
|
Title: Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Volume: Chapter 21 ISSN: 1934-3647 ISO Abbreviation: Curr Protoc Mol Biol Publication Date: 2012 Oct |
Date Detail:
|
Created Date: 2012-10-02 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 8908160 Medline TA: Curr Protoc Mol Biol Country: United States |
Other Details:
|
Languages: eng Pagination: Unit21.24 Citation Subset: IM |
Affiliation:
|
Pennsylvania State University, University Park, Pennsylvania. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Using Cell-ID 1.4 with R for microscope-based cytometry.
Next Document: Carbohydrate recognition and photodegradation by an anthracene-Kemp's acid hybrid.