Mapping of genomic interactions

1. A method, comprising:

a) contacting a first cell with a test compound; and

b) generating a carbon copy chromosome capture (5C) library from said first cell using the method comprising:

i) providing a chromosome conformation capture (3C) library constructed from cross-linked interacting chromatin segments derived from at least one cell, wherein said 3C library comprises a plurality of ligation products representative of interacting genomic loci, wherein each of said plurality of ligation products is formed by two adjacent restriction fragments;

ii) annealing unique primer pairs to at least a part of said plurality of ligation products; and

iii) ligating said annealed unique primer pairs together, thereby providing a carbon copy chromosome capture (5C) library, and

c) comparing interaction frequencies in said carbon copy chromosome capture (5C) library with interaction frequencies in a second carbon copy chromosome capture (5C) library generated from a second cell not exposed to said test compound.

2. The method of claim 1 , wherein said plurality of unique primer pairs comprises at least 10 unique primer pairs.

3. The method of claim 1 , wherein said plurality of unique primer pairs comprises at least 100 unique primer pairs.

4. The method of claim 1 , wherein said plurality of unique primer pairs comprises at least 500 unique primer pairs.

5. The method of claim 1 , wherein said plurality of unique primers pairs comprises at least 1000 unique primer pairs.

6. The method of claim 1 , wherein said plurality of unique primers pairs comprises at least 10,000 unique primer pairs.

7. The method of claim 1 , wherein said plurality of unique primers pairs comprises at least 100,000 unique primer pairs.

8. The method of claim 1 , wherein said ligation products comprise nucleic acids approximately 100 bps in length.

9. The method of claim 1 , wherein said 5C library is representative of long-range genomic interactions.

10. The method of claim 9 , wherein said long-range genomic interactions comprise interaction of activators or repressors of gene expression with a gene.

11. The method of claim 9 , wherein said long-range genomic interactions comprise interaction of chromatin on different chromosomes.

12. The method of claim 1 , wherein said at least one cell is an animal cell.

13. The method of claim 1 , wherein said at least one cell is selected from the group consisting of a bacterial cell, and a plant cell.

14. The method of claim 1 , further comprising the step of calculating interaction frequencies for said long range genomic interactions.

15. The method of claim 1 , wherein said 3C library has one or more variant genes selected from at least one of the group consisting of polymorphisms, genomic deletions, genomic fusions, genomic translocations, and genomic inversions.

16. The method of claim 1 , further comprising step (d) amplifying said 5C library with a single pair of universal primers.

17. The method of claim 16 , further comprising step (e) analyzing said amplified 5C library with a high-throughput application.