MAPPING OF GENOMIC INTERACTIONS

• US 20100130373A1
• Filed: 08/24/2007
• Published: 05/27/2010
• Est. Priority Date: 08/24/2006
• Status: Active Grant

• Current Assignee: University Of Massachusetts
• Original Assignee: University Of Massachusetts
• Inventors: Dekker, Job, Dostie, Josee
• Granted Patent: US 9,273,309 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12N 15/1072 Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups

Abstract

The present invention relates to genomic analysis. In particular, the present invention provides methods and compositions for mapping genomic interactions.

Claims

1. A method, comprising:

a) contacting a genomic interaction library with a plurality of unique primers under conditions such that ligation mediated amplification generates a second genomic interaction library; and

b) amplifying said second genomic library with a single pair of PCR primers, wherein said single pair of PCR primers amplify all members of said second genomic library.

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

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

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

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

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

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

8. The method of claim 1, wherein said second genomic interaction library comprises nucleic acids approximately 100 bps in length.

9. The method of claim 1, wherein members of said second genomic interaction library are identified using high throughput sequencing.

10. The method of claim 1, wherein members of said second genomic interaction library are identified using a microarry.

11. The method of claim 1, wherein said genomic interaction library comprises sequences involved in long-range genomic interactions.

12. The method of claim 11, wherein said long-range genomic interactions comprise interaction of activators or repressors of gene expression with a gene.

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

14. The method of claim 1, wherein said genomic interaction library is derived from a cell.

15. The method of claim 14, wherein said cell is an animal cell.

16. The method of claim 14, wherein said cell is selected from the group consisting of a bacterial cell, a viral cell, and a plant cell.

17. The method of claim 11, further comprising the step of calculating interaction frequencies for said long range genomic interactions.

18. The method of claim 1, wherein said genomic interaction library is derived from a cell that has one or more variant genes selected from the group consisting of polymorphisms, genomic deletions, genomic fusions, genomic translocations, and genomic inversions.

19. A method, comprising:

a) contacting a cell with a test compound; and

b) generating a second genomic library from said cell using the method of claim 1, and

c) comparing interaction frequencies in said second genomic library with interaction frequencies in a second genomic library generated from a cell not exposed to said test compound.

20. A method, comprising;

a) contacting nucleic acid with a cross-linking agent under conditions such that interacting chromatin segments are cross-linked;

b) digesting said cross-linked chromatin segments to generate digested chromatin segments;

c) ligating said digested chromatin segments to generate a genomic interaction library;

d) contacting said genomic interaction library with a plurality of unique primers under conditions such that ligation mediated amplification generates a second genomic interaction library, and

e) amplifying said second genomic library with a single pair of PCR primers, wherein said single pair of PCR primers amplify all members of said second genomic library.