Methods of identifying interactions between genomic loci

1. A method for identifying interaction frequencies, comprising:

a) providing;

i) a nuclear matrix comprising a first genomic region and a second genomic region; and

ii) a junction marker labeled with an affinity marker for selective purification of a ligation product;

b) fragmenting said first genomic region and said second genomic region into a plurality of first genomic region fragments and a plurality of second genomic region fragments;

c) ligating said junction marker between at least one of said first genomic region fragments and at least one of said second genomic region fragments to create said ligation product;

d) purifying said ligation product with said affinity marker;

and

e) analyzing said ligation product under conditions such that a genomic interaction frequency for said ligation product is identified.

2. The method of claim 1 , wherein said affinity marker comprises biotin.

3. The method of claim 1 , wherein said first and second genomic regions are located on the same chromosome.

4. The method of claim 1 , wherein said first and second genomic regions are located on different chromosomes.

5. The method of claim 1 , wherein said interaction frequency identifies a long range interaction.

6. The method of claim 1 , wherein said interaction frequency identifies a short range interaction.

7. The method of claim 1 , wherein said interaction frequency identifies a close neighbor interaction.

8. The method of claim 1 , wherein said nuclear matrix is derived from a human cell nucleus.

9. The method of claim 1 , wherein said nuclear matrix is derived from a yeast cell nucleus.

10. The method of claim 1 , further comprising contacting said junction marker with a ligand.

11. The method of claim 10 , wherein said ligand comprises streptavidin.

12. The method of claim 1 , further comprising digesting said nuclear matrix fragments with a restriction endonuclease wherein a first region fragment comprising a first sticky end and a second region fragment comprising a second sticky end are created.

13. The method of claim 12 , further comprising filling in said first sticky end and said second sticky end to create a first blunt end and a second blunt end; and ligating said first and second blunt ends, wherein said first region fragment and said second region fragment are joined.

14. The method of claim 1 , further comprising digesting said nuclear matrix fragments with an exonuclease.

15. A method for identifying interaction frequencies, comprising:

a) crosslinking a nuclear matrix comprising a first genomic region and a second genomic region;

b) fragmenting said first genomic region and said second genomic region into a plurality of first genomic region fragments and a plurality of second genomic region fragments;

c) ligating a junction marker labeled with an affinity marker between at least one of said first genomic region fragments and at least one of said second genomic region fragments to create a ligation product;

d) purifying said ligation product with said affinity marker;

and

e) analyzing said ligation product under conditions such that a genomic interaction frequency for said ligation product is identified.

16. A method for identifying interaction frequencies, comprising:

a) crosslinking a nuclear matrix comprising a first genomic region and a second genomic region;

b) fragmenting said first genomic region and said second genomic region into a plurality of first genomic region fragments and a plurality of second genomic region fragments;

c) ligating a junction marker labeled with an affinity marker between at least one of said first genomic region fragments and at least one of said second genomic region fragments to create a ligation product;

d) purifying said ligation product with said affinity marker;

and

e) detecting a close proximity between said first genomic region and said second genomic region with said ligation product under conditions such that a genomic interaction frequency for said ligation product is identified.

17. A method for identifying interaction frequencies, comprising:

a) crosslinking a nuclear matrix comprising a first genomic region and a second genomic region;

b) fragmenting said first genomic region and said second genomic region into a plurality of first genomic region fragments and a plurality of second genomic region fragments;

c) ligating a junction marker labeled with an affinity marker between at least one of said first genomic region fragments and at least one of said second genomic region fragments to create a ligation product;

d) purifying said ligation product with said affinity marker;

and

e) identifying a contact probability as a function of genomic distance between said first genomic region and said second genomic region with said ligation product under conditions such that a genomic interaction frequency for said ligation product is identified.

18. A method for identifying interaction frequencies, comprising:

a) crosslinking a nuclear matrix comprising a first genomic region and a second genomic region;

b) fragmenting said first genomic region and said second genomic region into a plurality of first genomic region fragments and a plurality of second genomic region fragments;

c) ligating a junction marker labeled with an affinity marker between at least one of said first genomic region fragments and at least one of said second genomic region fragments to create a ligation product;

d) purifying said ligation product with said affinity marker;

and

e) identifying whether said first genomic region and said second genomic region preferentially associate with each other with said ligation product under conditions such that a genomic interaction frequency for said ligation product is identified.