Patent ID: 8076070

Claim:
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.