Title
Chromosome Conformation Capture (3C) in Budding Yeast
UMMS Affiliation
Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2015-06-01
Document Type
Article
Disciplines
Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics | Laboratory and Basic Science Research | Systems Biology
Abstract
Chromosome conformation capture (3C) is a method for studying chromosomal organization that takes advantage of formaldehyde cross-linking to measure the spatial association of two pieces of chromatin. The 3C method begins with whole-cell formaldehyde fixation of chromatin. After cell lysis, solubilized chromatin is digested with a type II restriction endonuclease, and cross-linked DNA fragments are ligated together. Cross-links are reversed by degradation with proteinase K, and chimeric DNA molecules are purified by standard phenol:chloroform extraction. The resulting 3C library represents chromatin fragments that may be separated by large genomic distances or located on different chromosomes, but are close enough in three-dimensional space for cross-linking. Locus-specific oligonucleotide primers are used to detect interactions of interest in the 3C library using end-point polymerase chain reaction (PCR).
DOI of Published Version
10.1101/pdb.prot085175
Source
Cold Spring Harb Protoc. 2015 Jun 1;2015(6):580-6. doi: 10.1101/pdb.prot085175. Link to article on publisher's site
Journal/Book/Conference Title
Cold Spring Harbor protocols
Related Resources
PubMed ID
26034304
Repository Citation
Belton J, Dekker J. (2015). Chromosome Conformation Capture (3C) in Budding Yeast. Program in Systems Biology Publications. https://doi.org/10.1101/pdb.prot085175. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/72