Chapter title |
Detection of Short-Range Chromatin Interactions by Chromosome Conformation Capture (3C) in Yeast.
|
---|---|
Chapter number | 13 |
Book title |
Yeast Genetics
|
Published in |
Methods in molecular biology, January 2014
|
DOI | 10.1007/978-1-4939-1363-3_13 |
Pubmed ID | |
Book ISBNs |
978-1-4939-1362-6, 978-1-4939-1363-3
|
Authors |
Badri Nath Singh, Michael Hampsey, Singh, Badri Nath, Hampsey, Michael |
Abstract |
We describe a modified 3C ("chromosome conformation capture") protocol for detection of transient, short-range chromatin interactions in the yeast Saccharomyces cerevisiae. 3C was initially described by Job Dekker and involves formaldehyde cross-linking to stabilize transient chromatin interactions, followed by restriction digestion, ligation, and locus-specific PCR. As such, 3C reveals complex three-dimensional interactions between distal genetic elements within intact cells at high resolution. Using a modified version of Dekker's protocol, we are able to detect gene loops that juxtapose promoter and terminator regions of yeast genes with ORFs as short as 1 kb. We are using this technique to define the cis- and trans-acting requirements for the formation and maintenance of gene loops, and to elucidate their physiological consequences. We anticipate that this method will be generally applicable to detect dynamic, short-range chromatin interactions, not limited to gene loops. |
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