Methods of detecting long range chromosomal interactions

Abstract

The present invention relates to a method of monitoring epigenetic changes comprising monitoring changes in conditional long range chromosomal interactions at at least one chromosomal locus where the spectrum of long range interaction is associated with a specific physiological condition, the method comprising the steps of:— (i) in vitro crosslinking of said long range chromosomal interactions present at the at least one chromosomal locus; (ii) isolating the cross linked DNA from said chromosomal locus; (iii) subjecting said cross linked DNA to restriction digestion with an enzyme that cuts at least once within the at least one chromosomal locus; (iv) ligating said cross linked cleaved DNA ends to form DNA loops; (v) identifying the presence of said DNA loops; wherein the presence of DNA loops indicates the presence of a specific long range chromosomal interaction.

1 - 5 . (canceled) 
     
     
         6 . A method of monitoring a change in a specific conditional long-range chromosomal interaction at a locus comprising ligating together DNA sequences from the regions of chromosomes that have come together in a chromosome interaction to thereby make ligated DNA,
 wherein the locus comprises a gene that is regulated by metabolic signalling which leads to an alternative expression from the gene due to a change in chromosome interaction at the locus, and   wherein the long-range chromosomal interaction is not an interaction between a gene and its regulatory elements.   
     
     
         7 . A method according to  claim 6  which is carried out by a chromosome conformation capture (3C) technique comprising the steps of:
 (i) in vitro crosslinking the specific conditional long range chromosomal interaction; 
 (ii) isolating the cross linked DNA; 
 (iii) subjecting said cross linked DNA to restriction digestion; and 
 (iv) ligating said cross linked cleaved DNA ends to form the ligated DNA. 
 
     
     
         8 . A method according to  claim 6  which further comprises PCR amplification of the ligated DNA. 
     
     
         9 . A method according to  claim 6  wherein said ligated DNA is a predefined ligated DNA of known identity. 
     
     
         10 . A method according to  claim 6  wherein the ligated DNA corresponds to a physiological state. 
     
     
         11 . A method according to  claim 10  wherein the physiological state corresponds to a condition selected from the group consisting of, a cardiovascular disorder, an inflammatory condition, an autoimmune disorder, an inflammatory response to an infectious disease, a cancer and an inherited genetic disorder. 
     
     
         12 . A method according to  claim 6  wherein said change in a chromosome interaction corresponds to decreased repression of expression from the gene. 
     
     
         13 . A method according to  claim 6  wherein said change in a chromosome interaction corresponds to expression of an altered product from the gene.