Genome-wide chromosome conformation capture
First Claim
Patent Images
1. A method of determining the three-dimensional arrangement of an entire genome in a cell, comprising:
- (a) contacting a cell with a cross-linking reagent to cross-link the chromatin and the proteins in the cell;
(b) lysing the cell;
(c) digesting the chromatin with a restriction enzyme to generate DNA fragments with free ends, wherein the DNA fragments are cross-linked to the proteins;
(d) ligating DNA linkers to all free DNA ends generated by the restriction enzyme;
(e) annealing the ends of the DNA linkers that are not ligated to the free DNA ends generated by the restriction enzyme;
(f) translating the nicks between the annealed ends of the DNA linkers;
(g) detaching the proteins cross-linked to the DNA fragments;
(h) extracting DNA;
(i) subjecting the extracted DNA to two rounds of parallel sequencing; and
(j) determining the three-dimensional arrangement of the entire genome in the nucleus of the cell.
1 Assignment
0 Petitions
Accused Products
Abstract
The invention relates to the use of GCC (Genome Conformation Capture) technology in determining the three dimensional arrangement of an entire genome.
-
Citations
15 Claims
-
1. A method of determining the three-dimensional arrangement of an entire genome in a cell, comprising:
-
(a) contacting a cell with a cross-linking reagent to cross-link the chromatin and the proteins in the cell; (b) lysing the cell; (c) digesting the chromatin with a restriction enzyme to generate DNA fragments with free ends, wherein the DNA fragments are cross-linked to the proteins; (d) ligating DNA linkers to all free DNA ends generated by the restriction enzyme; (e) annealing the ends of the DNA linkers that are not ligated to the free DNA ends generated by the restriction enzyme; (f) translating the nicks between the annealed ends of the DNA linkers; (g) detaching the proteins cross-linked to the DNA fragments; (h) extracting DNA; (i) subjecting the extracted DNA to two rounds of parallel sequencing; and (j) determining the three-dimensional arrangement of the entire genome in the nucleus of the cell. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
-
-
2. The method of clam 1, wherein the cross-linking reagent is formaldehyde.
Specification