Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis
UMass Chan Affiliations
Program in Systems BiologyDepartment of Biochemistry and Molecular Pharmacology
Document Type
Journal ArticlePublication Date
2018-09-04Keywords
BiochemistryGenetic Phenomena
Genetics and Genomics
Investigative Techniques
Laboratory and Basic Science Research
Molecular Biology
Systems Biology
Metadata
Show full item recordAbstract
In all 3C-based assays, the aim is to measure the frequency with which two loci interact within cells. This is achieved by determining the relative abundance of ligation products formed during the 3C protocol that carry sequences from both loci. Individual 3C ligation products that are present in a 3C library, the ChIP-loop library, or the control library can be detected by polymerase chain reaction (PCR) using locus-specific primers. The following protocol outlines the procedure to measure relative abundances of ligation products in these libraries using PCR. The first part of the protocol-library titration-is required only once to determine the linear range of PCR detection. Once the linear range of PCR detection is known for a given ligation product library, follow the second part-interaction analysis-to measure the abundance of ligation products of interest in that library. Specific issues regarding determining the relative abundance of ligation products, designing PCR primers, and quantifying interaction frequencies are also described.Source
Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097873. doi: 10.1101/pdb.prot097873. Link to article on publisher's site
DOI
10.1101/pdb.prot097873Permanent Link to this Item
http://hdl.handle.net/20.500.14038/49874PubMed ID
30181221Related Resources
ae974a485f413a2113503eed53cd6c53
10.1101/pdb.prot097873