Mapping of genomic interactions

A method for mapping genomic interactions, comprising:

• a) 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 ligated nucleic acid restriction fragments with a junction representative of interacting genomic loci;
• and
• b) performing multiplex ligation mediated amplification with primer pairs targeting said junction;
• and
• c) creating a genomic interaction map based upon a plurality of multiplex ligation mediated amplification products.

A method for mapping genomic interactions, comprising:

• a) contacting deoxyribonucleic 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 first genomic interaction library comprising a plurality of ligation products;
• d) contacting said plurality of ligation products with a plurality of unique primers under conditions such that ligation mediated amplification generates a second genomic interaction library that is a copy of a part of said first genomic interaction library;
• e) amplifying said second genomic library with a single pair of PCR primers;
• and
• f) creating a genomic interaction map based upon said second genomic library.