Genome-wide chromosome conformation capture

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.

2. The method of clam 1 , wherein the cross-linking reagent is formaldehyde.

3. The method of claim 1 , wherein the DNA linkers contain a palindromic overhang on one end and a T overhang on the other end.

4. The method of claim 3 , wherein the DNA linkers are ligated to the free DNA ends generated by the restriction enzyme through the T overhang.

5. The method of claim 3 , wherein the DNA linkers are ligated to the free DNA ends generated by the restriction enzyme by T4 DNA ligase.

6. The method of claim 1 , further comprising adjusting the ligation mixture after step (d) to highly favor intramolecular reactions.

7. The method of claim 1 , wherein the ends of the DNA linkers being annealed in step (e) are adjacent due to the DNA linkers being ligated to the DNA fragments that are cross-linked to the proteins.

8. The method of claim 1 , wherein the nicks are translated with E. coli DNA polymerase I.

9. The method of claim 1 , wherein the nicks are translated in both directions along the DNA fragments until they arrive at cross-linked sites.

10. The method of claim 1 , further comprising adding phosphothioate-containing nucleotides to a second round of nick-translation.

11. The method of claim 1 , wherein the proteins cross-linked to the DNA fragments are detached by heating at 65° C. over night.

12. The method of claim 1 , wherein the DNA is extracted with phenol:chloroform.

13. The method of claim 1 , further comprising removing DNA that has not gone through steps (d) and (e) and free DNA linkers after step (h).

14. The method of claim 13 , wherein the DNA that has not gone through steps (d) and (e) and free DNA linkers are removed by a phosphothioate-sensitive exonuclease.

15. The method of claim 1 , wherein the extracted DNA is sequenced using the Illumina/Solexa platform.